In the ‘Match at Mission Hills’, at a sprawling golf complex on Hainan Island, the Northern Irish world number six shot six-under-par 66 to Woods’ 67 in the one-round face-off.
McIlroy, who has dropped off the top of the rankings and has not won a tournament all year, also beat Woods by one shot in a similar Chinese event last year.
Monday’s victory, at the same venue where he won the World Cup with Graeme McDowell in 2011, will give him a boost ahead of this week’s WGC-HSBC Champions in Shanghai.
“I would like to play all my tournaments in China where I can beat Tiger,” said the 24-year-old. “It’s been great to come back to this wonderful golf course where I still have such great memories.”