The Bears (16-7, 8-0 Mid-Eastern Athletic Conference) jumped out to a 14-4 lead after two free throws by Rodney Stokes with 13:08 left in the first half and didn't trail the rest of the way.
The Aggies (7-15, 3-5) committed seven turnovers during Morgan State's opening spurt, and finished with 15.
The Bears scored 22 points off turnovers in their eighth straight win.
Morgan State committed 20 turnovers leading to 15 Aggies' points, but outrebounded North Carolina A&T 51-33.
Troy Smith scored 16 points and Thompson finished with 10 for the Bears. Holmes, the MEAC Player of the Week, was 9 of 16 from the field and 4 of 9 from 3-point range.
The Aggies were led by Tavarus Alston with 23 points and Thomas Coleman with 11.