HILTON HEAD ISLAND, 18 Apr 2015 (AFP) - The American went into the round with a four-stroke lead after a course record-equalling 61 on Friday.
His 54-hole total of 14-under-par 199 put him three shots clear of a trio of players.
Defending champion Matt Kuchar, who played in the last group with Merritt, carded a 68 for 202. Brendon Todd joined the group sharing second with a sparkling 63 and Kevin Kisner posted a 67 to get to 11-under for the tournament.
Todd's 63 -- the third lowest round of the week after Merritt's 61 and Jordan Spieth's 62 -- included eight birdies without a bogey.
Five of his birdies came on the front nine at Harbour Town Golf Links and he added two more at 11 and 16 before chipping in for birdie at the par-four 18th.
"I came up a little short with the six-iron coming into the green and had a long chip with a lot of green," Todd said. "I used my pitching wedge and it went right at the hole. I was fortunate to get it on line there."
It was a further stroke back to another group of three on 203: former champion Jim Furyk (68), Brice Garnett (65) and Branden Grace (66).
Masters champion Spieth followed up his second-round 62 with a 68 that kept him in the hunt on 204, tied with fellow American Bo Van Pelt, who carded a 67.
Merritt's round included four birdies and a double-bogey six at the par-four eighth, where he was in the water with his second shot but rolled in a tough five-foot putt to limit the damage.
"It was one good shot on the hole," Merritt said of the putt. "It was just a momentum keeper.
"I was hitting the ball just fine all day and I just tugged a six-iron, something that hasn't happened in a while, and watched it sail into the water and make a spectacular splash," he said.
"But I was able to roll that five- six-footer in and keep the momentum going."
Merritt responded with his third birdie of the round at the par-four ninth, and picked up one more stroke coming in when he struck his tee shot within four feet at the par-three 14th and rolled in the birdie putt.
Sunday's final round will tee off earlier than originally scheduled, with groups going off from the first and 10th tees as organizers try to beat the thunderstorms forecast for the afternoon in South Carolina.
Leading third-round scores on Saturday in the US PGA Tour $5.9 million RBC Heritage (USA unless noted):
199 - Troy Merritt 69-61-69
202 - Brendon Todd 73-66-63, Kevin Kisner 68-67-67, Matt Kuchar 68-66-68
203 - Brice Garnett 72-66-65, Branden Grace 70-67-66, Jim Furyk 71-64-68
204 - Bo Van Pelt 69-68-67, Jordan Spieth 74-62-68
205 - Luke Donald (ENG) 73-66-66, Brendon de Jonge (ZIM) 70-68-67, Justin Thomas 70-67-68, Louis Oosthuizen (RSA) 69-67-69, Morgan Hoffmann 68-68-69, John Merrick 69-65-71, Graeme McDowell (NIR) 66-69-70
206 - Ian Poulter (ENG) 69-70-67, Russell Knox (SCO) 75-64-67, Matt Every 66-70-70
207 - Jason Kokrak 72-70-65, Jason Dufner 74-67-66, Pat Perez 69-71-67, Sean O'Hair 70-67-70, Lucas Glover 70-67-70, Kevin Streelman 71-65-71, Jerry Kelly 71-66-70