Reigning champion van Gerwen is aiming to collect a third triumph in the double-start tournament at the Citywest Hotel, but overcame an early scare before seeing off Huybrechts.
The Belgian ace came from a leg down to win the opening set 3-1 with the aid of two 180s, and also came from two legs down to send the second set into a decider.
Van Gerwen, though, fired in a key maximum as he edged the set 3-2 to level before replying to Huybrechts winning the third set's opener with a 160 checkout.
That finish was followed by a missed bullseye from Huybrechts in the third leg as a third-dart double 16 moved van Gerwen 2-1 up and double ten sealed the set before the world number one raced through set four without reply to complete his fight back.
"I'm really glad I won but it wasn't the performance I wanted and I struggled to hit double top at times," said van Gerwen, the 2012 and 2014 champion. "I felt fantastic in the practice room but I was a bit nervous when I got on stage.
"I didn't want to lose and I'm still in the tournament, which is the most important thing. I was annoyed with my own game because I can perform a load better than this but the win will give me confidence.
"I want to retain this title and make this the hat-trick, and I know I can do that."
Van Gerwen now meets Jamie Lewis in the quarter-finals, after the Welsh youngster knocked out Michael Smith in one of three other second round games which saw a player from the world's top ten eliminated.
Number eight seed Smith made a superb start by winning the opening set without reply - including checkouts of 96 and 92 - before edging the second set 3-2.
Lewis, though, took out 95 to win the deciding leg of the third set before taking the fourth 3-1 to send the game into a one-set shoot-out.
Smith led 1-0 as the Welsh ace missed three darts at doubles, but Lewis regained his composure to take the next two before winning the deciding leg with a superb 108 finish to reach his first major TV quarter-final.
"I'm over the moon," said Cardigan-based Lewis. "At 2-0 down I thought it was game over so I'm really chuffed to come back and win.
"I felt a bit edgy and at 2-0 down I had nothing to lose. I've learned over the years that at 2-0 down the game's not over until they hitting the winning double, so that was in my head tonight and I managed to get the job done in the end.
"I'm really pleased. In the last year or so, I've felt as if I belong playing in the TV majors and I'm trying to make myself an established player, and it's going well so far."
World number five Adrian Lewis suffered a straight sets defeat to an inspired Mark Webster, who won through to his first major quarter-final for 18 months as he averaged almost 92 in the double-start format in a confident display.
The Welsh left-hander swept through the first set without reply and came from a leg down to win the second 3-1 courtesy of a 104 checkout in the fourth leg.
Lewis shared the opening two legs of the third set, but Webster landed a key 180 in the third leg before hitting tops in the next to seal his last eight spot.
"It was a solid performance and it's great to be in the quarter-finals," said Webster. "Adrian wasn't at the races but I was there to take my chances and I did the job.
"I've shown before that I can beat these big players if they don't perform, and I'm in the quarter-finals now and enjoying it.
"I've got Jelle Klaasen next and it's going to be tough but I've got the game to beat him, and I've got nothing to lose. He'll start as the favourite and I'm happy being the underdog, so I've got to pile on the pressure and make him think."
Webster will now face a fellow former Lakeside Champion, Jelle Klaasen, in Thursday's quarter-finals after the Dutchman saw off Dave Chisnall in a five-set thriller.
After Klaasen won the opening leg with a 13-darter, Chisnall levelled with a 103 finish and edged the set in the deciding leg, only for his opponent to take the next two sets with 3-1 scorelines, finishing 129, 134 and 132 in the process.
Klaasen also took out 100 in the fourth set, but Chisnall held his nerve in the fifth leg to take out a key 71 as he sent the match into a decider.
Klaasen, though, landed two 180s and a 177 as he took the set 3-1 to continue his fine year on the circuit with a first Dublin quarter-final.
"I'm feeling very good but it was such a tough game," said Klaasen. "I didn't miss many doubles to start the legs and I finished well, so I'm very happy with my game.
"In the middle of the game Dave out-scored me a bit and I needed the big finishes, so luckily I hit them."
Klaasen added: "Two years ago I didn't win a leg against Gary Anderson, so to be in the quarter-finals is the result of all the work I've put in. I've practised a lot for the past 18 months and it's paying off.
"I feel good, and if I keep hitting double 18 like I did in this game then I can go far."
The second round concludes on Wednesday evening with the remaining four games, including Vincent van der Voort taking on Terry Jenkins two days after the Dutchman knocked out Phil Taylor.
World Champion Gary Anderson plays Ian White, Robert Thornton opens up against Justin Pipe and Mensur Suljovic takes on Simon Whitlock.
The partypoker.com World Grand Prix will be broadcast live on Sky Sports and worldwide through the PDC's series of international broadcast partners, and through www.LIVEPDC.TV for International Pass Subscribers.
Tickets for the partypoker.com World Grand Prix are available from the Citywest Hotel by email email@example.com or by calling 01 401 0505 (Outside Ireland 00353 1 401 0505).
partypoker.com World Grand Prix
Tuesday October 6
Michael Smith 2-3 Jamie Lewis
Dave Chisnall 2-3 Jelle Klaasen
Michael van Gerwen 3-1 Kim Huybrechts
Adrian Lewis 0-3 Mark Webster
Wednesday October 7 (7pm)
Robert Thornton v Justin Pipe
Mensur Suljovic v Simon Whitlock
Vincent van der Voort v Terry Jenkins
Gary Anderson v Ian White
Second Round - Best of five sets
* All Sets are the best of five legs. There will be no tie-break in any set.
* All legs must begin and end with a double, meaning that a player must hit a double before he can begin scoring in each leg.
Michael Smith v Jamie Lewis
1-0 - Double ten gives Smith the opening leg.
2-0 - A 96 checkout for Smith sees him move two legs clear.
3-0 - Smith fires in a 180 before finishing 92 to claim the set in a fine start.
1-0 - Smith's superb opening continues as he posts tops to lead in set two.
1-1 - Smith lands a 180, but Lewis posts double five to claim his first leg of the game.
2-1 - Lewis misses the bull to finish 85, and Smith takes out 75 on double 12.
2-2 - Lewis hits a 180 and takes out 92 to level the set.
3-2 - Smith replies with a 180 before taking the set on double ten to move two sets up.
0-1 - Smith sets up a possible nine-dart finish by scoring 160 and 171 to leave 170 - but after missing out on a nine-darter he sees Lewis claim the leg.
1-1 - The roles are reversed as Lewis hits a 180 but misses three doubles, allowing Smith in on double nine.
1-2 - Lewis hits another maximum before moving back ahead.
2-2 - Smith posts a 180 and double six to level, moving a leg away from the win.
2-3 - Lewis keeps the game alive by winning the deciding leg, despite a 180 from his opponent, with a 95 finish.
1-0 - Smith powers in a 180 for a third successive leg before finishing 48.
1-1 - Tops sees Lewis level.
1-2 - Lewis lands double 16 to move ahead in the set.
1-3 - Lewis hits a 180 and double eight to square the game at two sets all.
1-0 - Lewis fires in a 174 score to leave 16, but misses three doubles to allow Smith in tops.
1-1 - Smth hits another maximum, but six missed doubles allow Lewis in on tops to level the set.
1-2 - Further misses from Smith allow Lewis to hit double eight to lead for the first time in the game.
2-2 - Smith hits back to send the game into a deciding leg, opening with a 160 score before finishing double ten.
2-3 - Lewis completes his superb fightback by taking out 108 on double 16 to reach his first major quarter-final.
Dave Chisnall v Jelle Klaasen
0-1 - Klaasen makes an ideal start, landing a 180 in a 13-darter which he finishes on double 18.
1-1 - Chisnall takes out 103 to level.
1-2 - Klaasen lands a 171 score as he edges back ahead.
2-2 - Double 18 for Chisnall sends the set into a deciding leg.
3-2 - Klaasen lands a 180 but misses the bull to finish 90, allowing Chisnall in on double eight to edge the set.
1-0 - Chisnall holds throw to claim the second set's opener.
1-1 - Chisnall sets up a possible nine-dart finish by opening with a 160 and adding a 180 - but after missing out on a nine-darter sees Klaasen finish 129 on the bull to take the leg.
1-2 - Klaasen takes out 75 to move ahead.
1-3 - Chisnall's miss at double 16 allows the Dutchman to take the set and level the match.
1-0 - Chisnall finishes double 16 to move ahead.
1-1 - Klaasen opens with a 156 score before defying a Chisnall with a 180 with a superb 134 finish.
1-2 - Klaasen moves ahead by taking out 97 on double 12.
1-3 - A thrilling 132 bull finish gives Klaasen the set and a 2-1 lead.
1-0 - A 24 finish sees Chisnall move in front in the fourth set.
1-1 - Klaasen again kicks off with a 156 score before taking out 100 for an 11-darter.
2-1 - Chisnall takes out double ten to move ahead.
2-2 - Klaasen's 74 checkout moves him a leg away from the win.
3-2 - Chisnall kicks off with a 160 score before finishing 71 with two pressure darts to send the tie into a fifth set.
0-1 - Klaasen lands his third 180 of the game and finishes 56 to lead in the deciding set.
1-1 - The pair trade maximums before Klaasen's miss at double 18 allows Chisnall in on double ten to square the game.
1-2 - Klaasen lands a third 180 in as many legs before double nine moves him a leg away from the win once again.
1-3 - Klaasen hits a 177 before Chisnall hits a 171 score - but the 2013 runner-up misses tops to keep the game alive, and Klaasen returns on double 18 to seal the win.
Michael van Gerwen v Kim Huybrechts
1-0 - van Gerwen finishes 61 on double 18 to make a confident start.
1-1 - Huybrechts replies in kind with a 61 checkout on double 16.
1-2 - Huybrechts fires in a 180 before finishing eight to move ahead.
1-3 - A second break of throw sees Huybrechts claim the set, landing another maximum and double eight.
1-0 - Huybrechts lands another 180 but four missed doubles allow van Gerwen to snatch the leg on double ten.
2-0 - van Gerwen scores 174 before finishing 60 to break and move two legs up.
2-1 - The Belgian keeps the set alive with a 63 finish.
2-2 - The pair trade 180s before Huybrechts levels the set with a 76 checkout.
3-2 - van Gerwen pulls clear in the deciding leg, landing a 180 before returning to claim the set on double five.
0-1 - van Gerwen opens the set with a 160 score, but missed doubles allow Huybrechts to hold throw.
1-1 - van Gerwen this time takes out 160 in superb fashion to level.
2-1 - The Dutchman fires in a 180 before punishing Huybrechts' missed bullseye by landing double 16 to break.
3-1 - van Gerwen fires in double ten to claim the set.
1-0 - Double 18 sees van Gerwen continue his charge.
2-0 - van Gerwen fires in two 180s, and when Huybrechts wires double 12 the Dutchman takes out double 16 to win a fifth straight leg as he moves to the brink of victory.
3-0 - van Gerwen seals his place in the quarter-finals on double six.
Adrian Lewis v Mark Webster
0-1 - Webster claims the opening leg on top.
0-2 - The left-hander finishes 64 on tops to double his lead.
0-3 - Webster finishes 60 on double ten to win the opening set without Lewis having a dart at a finishing double.
1-0 - Lewis finishes 86 to claim his first leg of the game.
1-1 - Lewis fires home a maximum, but Webster takes out 54 to level.
1-2 - Webster has enough cushion to recover from misses across two visits to move ahead.
1-3 - Webster kicks off the leg with a 160 score before finishing 104 on tops to claim a two-set lead.
0-1 - Lewis opens the leg with a 160 score, but Webster fires in a maximum before hitting double ten to lead.
1-1 - Lewis finishes 66 to level the set.
1-2 - Webster fires in a maximum before taking out 68 to move a leg away from the win.
1-3 - Lewis leaves a double with a 171, but Webster seals a superb victory with tops, reaching his first major quarter-final since the 2014 World Championship.