The Crusaders (4-3) never trailed and led by as many as 17 in the second half, but New Hampshire (2-4) cut it to 57-52 with 1:59 left in the game. Holy Cross then scored the game's final six points, all free throws by Thompson. Thompson finished 10-of-10 on free throws despite the rest of the team going just 3-of-11 from the line.
New Hampshire shot 36.4 percent from the field and grabbed just four offensive rebounds in its fourth straight loss.
Holy Cross beat New Hampshire 60-50 last November, the last time the two teams faced.
Louisville's Chinanu Onuaku, who recently underwent a medical procedure to correct a heart rhythm issue detected during the combine, will keep his name in the NBA draft pool.
Andrew White III will return to the Nebraska men's basketball team next season after removing his name from the NBA draft.
Mike Brey is looking at former Notre Dame players to fill two assistant jobs that have opened up with the departures of Martin Ingelsby and Anthony Solomon.