Lee, born in Brazil to Korean parents, mixed eight birdies with a lone bogey in the penultimate round for a 54-hole total of 19-under 197, a shot ahead of defending champion Wood (65) and China's Hu Mu (64).
Scotland's Simon Yates shot a 64 on his 43rd birthday and overnight leader Scott Strange of Australia carded a 68 to be two shots behind the leader.
Triple major champion Harrington plummeted down the leaderboard with a three-over 75 and the Irishman now trails Lee by 11 strokes.
The 25-year-old Lee, seeking his first win on a major circuit, said he had tried to put the status of his playing partners to the back of his mind during his composed third round where he signed off with a birdie.
"After the first hole you try to forget who they are and try to beat them like any other of the guys, but they do hit the ball very well," Lee told the official website (www.oneasia.asia).
"It was a good learning experience. Tomorrow I'm just going to try and be as positive as possible, while also keeping it simple."
Englishman Wood said it would take another low score on Sunday at the Greg Norman-designed course to make it two in a row at the $1 million event which is co-sanctioned by the Japan Golf Tour Organisation and OneAsia.
"I'm really pleased with my efforts so far. I came here to put in a good defence," said the world number 64. "It will take something in the mid 60s to win."
Japan's Katsumasa Miyamoto, who started on the 10th hole, equalled the course record with a 63 after making the turn on 29 with seven birdies.