The Northern Irishman vaulted into a two-shot lead ahead of five-time major winner Phil Mickelson, American Justin Thomas and England's Ross Fisher.
Four-time major champion McIlroy reached a total of nine-under 133 at the Chapultepec Golf Club for his first 36 hole lead on the USPGA Tour since the 2014 PGA Championship at Valhalla.
"I just felt like I had a bit more energy. I had a bit more pep in my step," said McIlroy, who showed no ill effects of the stomach trouble he has battled this week. "I wasn't just trying to get through the round today. I was trying to build on the score that I had, and it was nice to feel like that again."
For a victory to propel McIlroy back to number one in the world, current number one Dustin Johnson would have to finish in a tie for fourth or worse.
Johnson was also in the hunt after a five-under 66 that put him in a three-way tie for fifth on 136 with England's Andy Sullivan (65) and Daniel Berger (66).
A group of seven players, including Thomas Pieters (69) and Martin Kaymer (67) were four shots back at five-under 137.
"Look, I'm in a great position. But I felt like I could have been a few more ahead," said McIlroy.
McIlroy already has two WGC victories on his resume, the 2014 Bridgestone and the 2015 WGC-Cadillac Match Play in San Francisco. He is trying to join Tiger Woods (18), Johnson (three) and Geoff Ogilvy (three) as the only players with three or more wins in World Golf Championships events.
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Johnson played in the marquee trio Friday with McIlroy and Japan's Hideki Matsuyama who shot his second straight 72.
Johnson, who moved to number one with his victory at Riviera Country Club two weeks ago, capped his round with his seventh birdie of the day at 18. He had a bogey at 14 but then made birdie on three of his final four holes to keep McIlroy in his sights.
"I feel like I am playing well," Johnson said. "I have just been struggling on the greens. It feels like someone is playing goalie up by the hole."
Mickelson will play with McIlroy on Saturday, the first time they have been paired together.
Thomas is aiming for his fourth victory of the 2016-17 season.
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