Choi's 65 was the lowest-ever third-round score in tournament history and tied the mark for the third-lowest round ever at a U.S. Women's Open.
The world No. 5 finished 54 holes at Blackwolf Run in Wisconsin at 8-under 208, leaving her closest competitor, Amy Yang (3-under 69), in the dust at minus-2.
Seventeen-year-old phenomenon Lexi Thompson fell into a tie for third place after managing an even-par 72. There she was joined by Mika Miyazato (73) and Sandra Gal (74) at 1-under 215.
Second-round leader Suzann Pettersen, meanwhile, stumbled to a 6-over 78 thanks in part to a pair of double-bogeys.