The Crusaders led 6-0 after the first quarter after a four-yard touchdown run by Dane Rutz.
MCC added two more scores in the second quarter on a one-yard TD run by Tiovanni Knight and a 15-yard touchdown pass from Max Price to Nolan Convertini.
Muskegon Heights got on the board before halftime with a 63-yard touchdown pass from Sylvester Kirks to Arlester Sims.
The Crusaders led 19-6 at halftime.
Muskegon Catholic pulled away in the fourth quarter with touchdowns from Rutz (24-yard run), Convertini (16-yard pass from Price), and two more from Rutz (five-yard run and 37-yard interception return).
MCC also collected two points on a safety.
Knight finished with 122 yards rushing on 15 carries with one touchdown. Rutz totaled 98 yards on 16 carries with three scores.
The Crusaders are now 3-3 overall and 2-1 in conference play. They will travel to Manistee next week for a conference showdown. A victory would give them a share of the Lakes 8 title.
MCC needs to win all three of its final games to qualify for the state playoffs.
Muskegon Heights fell to 0-6 and 0-3. The Tigers will visit Orchard View next week.