The South Korean player had a 13-under 200 total after opening with rounds of 65 and 67 at Kuala Lumpur Golf and Country Club.
"Actually, honestly, I don't like leading, that feeling. I like chasing better," Choi said. "But like today, I think I played too much safely. So tomorrow, I'm not going to think about my score, even two-shot lead. I just go out there with a general score and play my game. I want to play lower than any day."
She birdied the first hole before play was delayed for more than four hours because of lightning and rain, and finished with four birdies and a lone bogey on the 10th hole. For the third time in two years, the lights at course were turned on to help players finish.
"I think I had a pretty hard time today," Choi said. "It was raining all day. That's why I play so long. We wake up like 12 hours ago and that's a pretty long day. I have to focus on my game, play my game, just play one shot at a time. I think that's my goal tomorrow."
She won the U.S. Women's Open in July for her first major title and sixth LPGA Tour victory.
South Korea's Inbee Park, the tour money leader, was second after a 65.
"I think I played much better in the rain than hot," Park said. "The front nine was a little bit disappointing but I just knew the birdies would come out. I just tried to trust myself.
"I think I still need a lot of birdies tomorrow to win. I'll just go out there and play aggressive and try to get myself a lot of birdies."
Australia's Karrie Webb was four strokes back after a 68.
Norway's Suzann Pettersen was 8 under, following her second-round 64 with a 70. She was in contention and only a stroke behind Choi at the turn, but had a double bogey on the 15th and a bogey on the 16th.
Japan's Ai Miyazato also was 8 under after a 68.
The tournament opens the tour's four-event Asian swing. The HanaBank Championship is scheduled for next week in South Korea, followed by stops in Taiwan and Japan.