McIlroy, who finished his second round in the morning, surprisingly struggled for the first time in seven rounds into his comeback from a three-month layoff, and was 1-over par at the turn in the third round.
"I just wanted to play by myself and play my game".
The four-time major champion then recovered with five birdies on the back nine for a 4-under 68 and 19 under overall that put him one behind Li.
The Northern Irishman made his return from a hip injury at the Abu Dhabi HSBC Championship last week, where he placed joint-third.
Englishman Danny Willett endured a hard opening day as he dropped three shots on the eighth and another four on the ninth to finish five-over at the bottom of the leaderboard. "The quality of the golf was much better, which I was happy with, and to come back in five-under is very nice".
Given he was out in the afternoon's last group with McIlroy and Welshman Jamie Donaldson, it was an extremely impressive showing.
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After getting to 12-under, Scott Jamieson finished bogey-double bogey to sit alongside Richie Ramsay, with two-time victor Stephen Gallacher two shots behind his compatriots on six-under.
"Hopefully I can do my best out there and have some low scores".
"The back nine's been good to me this week", said the four-time major victor.
"I feel like if I play my game I'll be able to shoot something a bit lower tomorrow and I feel like I will need something a bit lower to win", McIlroy told Sky Sports after his third round.
Round of the day went to Andy Sullivan, the Englishman surging up the leaderboard with a 63, leaving him on -16, four adrift of Li but Donaldson's challenge faltered with a three-over 75. "This is a place I've always done well at hopefully that experience of winning a couple of times around here and being in contention quite a lot will help". "So just stayed patient all day".
"I'm looking forward to it", McIlroy said.