She posted a 17-under 199 total with one round left, while Duncan also shot 67 to move into second place alone on 16-under.
Duncan has never had a top-10 finish on the LPGA.
South Korean Chun In-gee, the 2015 U.S. Women’s Open champion, carded 68 to trail by two strokes, while Thai world number two Ariya Jutanugarn had the day’s best score, a 65, to jump within three shots with Canadian halfway co-leader Alena Sharp (70).
“Today was a lot windier than the last two days, so there was just more shot making and some pins were pretty difficult to get to,” Thompson told reporters. “It was more just making pars. I'm playing very well and making some good putts, so hopefully just continue that tomorrow.”
Thompson, 22, made headlines at the ANA Inspiration major two months ago, when she was penalised four strokes after it came to light she had mismarked her ball on a green during the third round.
She was docked two strokes for the infraction, and two more because she had signed an incorrect scorecard before the incident was brought to the attention of officials.
Thompson subsequently lost in a playoff, and her situation aroused sympathy with many golf fans, though not so much with insiders.
(Reporting by Andrew Both in Cary, North Carolina, editing by Gene Cherry)
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