Thompson finished 54 holes at 13-under-par 203 at Guadalajara Country Club.
She also won the Sime Darby LPGA Malaysia last month.
Holding sole possession of second place at 12-under was I.K. Kim, who recorded her own 67 Saturday.
Stacy Lewis grabbed the third position at minus-11 after also firing a 67.
Second-round co-leader So Yeon Ryu held fourth place at 10-under 206 with a third-round 1-under 71.
Anna Nordqvist and Pornanong Phatlum, who shared the second-round lead with Ryu, each notched a 72 to knot for fifth place at 9-under.