Robert Champion hit a 3-pointer with 2:45 left to extend Holy Cross' lead to 48-42. Corey Johnson answered with a 3-point shot and Zena Edosomwan's free throw pulled Harvard within 48-46 with 1:22 remaining. But Thompson made two free throws for a 50-46 lead.
Thompson finished with 13 points for Holy Cross (3-3) and Champion had 11.
Holy Cross opened the second half on an 8-3 run, with four points from Thompson, to take a 29-26 lead.
Patrick Steeves had six points, 12 rebounds and seven assists for Harvard (2-4). The Crimson were 19 of 51 (37 percent) from the field, including 8 of 24 from 3-point range. Tommy McCarthy, Steeves, Corbin Miller and Johnson had two 3's apiece.