The Eagles (3-0) are off to their best start since winning their first three games in 2008-09 when then-coach All Skinner's team finished 22-12. Dennis Clifford added 12 rebounds for the Eagles.
Zena Edosomwan led the Crimson (1-3) with 20 points and nine rebounds. Tommy McCarthy added 13 points.
Trailing 29-28, the Eagles went on a 12-2 run over the ensuing three minutes to grab the lead for good. Milon hit a pair of 3s during the spree.
BC pushed its lead to 52-42 on Milon's driving basket with 7 1/2 minutes left and was never threatened the rest of the way.
Carter missed all six of his shots from the floor in the first half, but nailed a pair of 3-pointers just over a minute apart early in the second for his first two baskets of the game.
Harvard scored the final six points of the first half to take a 20-16 edge into intermission.
Both teams shot under 40 percent in the first half, with BC hitting only 24 percent (6 of 25), and missing 7 of 10 on 3-point attempts. The Crimson shot 36.4 percent (8 of 22), and hit all three of their attempts beyond the arc.
Harvard: Beat Boston College six-straight times before losing in overtime last season.
Boston College: Carter started his last game 0-for-7 from the field before finishing with a team-high 18 points. . Backup center Idy Diallo fouled out in six minutes. . The Eagles had more turnovers (8) than baskets in the first half.
Harvard: Hosts Bryant on Wednesday.
Boston College: Faces No. 13 Michigan State at the Wooden Legacy in Anaheim, Ca. on Thursday.