The Northern Irishman used an astonishing display of long driving to overpower Quail Hollow, and struck a series of towering iron shots that honed in on the pins to set up 11 birdies.
He posted an 18-under 198 total, a tournament record low score, to open a four-shot lead over American Webb Simpson (68), and a seven-shot advantage over third-placed Robert Streb.
McIlroy's 61 bettered by one stroke the course record he held jointly with Brendon de Jonge.
McIlroy rated it among the best of his career.
"I looked at the scores in the morning and saw there were some low ones out there," the world number one told reporters.
"I got a little more aggressive, and it paid off.
"I just aimed at the flags today. It's as simple as that. I was taking dead aim."
The four-times major champion recalled he once shot a 61 at Portrush in Northern Ireland in an amateur event.
"That was a good round. There's been quite a lot of rounds where I've got it going but that was definitely up there today," said."
McIlroy had 23 putts, but did not hole anything longer than 15 feet and only once, at the first hole, where he sank a seven-footer for par, was he in serious danger of dropping a shot.
He started thinking about shooting a 59 after a birdie at the 13th took him to eight-under.
McIlroy needed to birdie the difficult final two holes to shoot a magical 59 but it was not to be as he left his approach shots a long way from the hole on both occasions.
"I was a little disappointed not finishing it off the way I wanted to," said McIlroy, who notched his first PGA Tour victory here five years ago.
He nearly did not play here this year, due to his busy schedule. He is glad he decided to come, even if it means playing five weeks in a row.
"I love the place, I'm playing well, so at least for now that decision (to play) has paid off," he said.
(Editing by Gene Cherry)
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