The Northern Irishman, who had been one ahead overnight after opening with a flawless 63, remained mentally upbeat despite two early bogeys and his positive attitude was rewarded with a four-under-par 66 at PGA National.
"It's just another 36-hole lead," McIlroy said after posting an 11-under total of 129, one ahead of Zimbabwean Brendon de Jonge (64) and three clear of American Russell Henley (68) on a day of contrasting fortunes for the big names.
Masters champion Adam Scott, who played with McIlroy for the first two rounds, made two double bogeys on the way to a 69 as he fell eight eight shots off the pace.
World number one Tiger Woods continued his recent struggles, making the cut with nothing to spare at even-par 140 after carding a 69, while Phil Mickelson will have the weekend off after shooting a 71 for a one-over total.
McIlroy, 24, has rediscovered his form in the past few months and says he is back at the comfort level he enjoyed in late 2012, when he was riding high atop the world rankings.
He changed driver and ball last autumn and sounds eminently satisfied with the results, saying he can hit a variety of shots with the new combination.
"I'm much more comfortable with everything and I think it shows in the way I'm playing," he said.
Not that it was all smooth sailing for the two-time major champion as he bogeyed his second hole (the par-four 11th) after a poor drive and then dropped another shot at the par-four 12th, where he missed the green with his approach.
"I think it's a sign of a little more maturity," McIlroy said of his ability to maintain an emotional even keel.
"I'm not trying to force the issue because I've made a couple of bogeys early. I knew had some opportunities coming up. I didn't panic. I just tried to keep playing the way I was.
"Now that I'm happy where my swing is, even if I do hit a loose shot I can get over it much easier and quicker."
McIlroy's putting has been stellar as well, just 49 putts to date, after he recently tweaked a couple of things during a refresher session with twice former PGA Championship winner Dave Stockton.
Woods, in only his ninth competitive round of the year, made several awful swings and needed a sharp short game to qualify for the weekend.
"It was a grind, no doubt about that," said the 14-times Major winner, who holed out for birdie from 15 yards at the par-four 13th before parring his way home.
"I hit a couple of loose iron shots coming in. I would like to hit it better than I have been but I fought out a number, which is always a good thing."
Woods, who has not won a major since the 2008 US Open, warned not to read too much into his mediocre early-season form as he gears up for the Masters in April, saying he took a "lot of positives" from his performance.
Mickelson, meanwhile, was happy with aspects of his game, but not the entire package.
"I had a hard time making birdies today," said the three-time Masters champion. "I drove the ball well. My iron play, distance control was off and I didn't putt as well as I expected."
For the second successive days, players were allowed preferred lies because of damp fairways.
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