Syracuse (13-5, 3-2 Big East), which lost 81-61 at West Virginia on Sunday and 74-66 at Cincinnati the previous game, has beaten Rutgers (8-10, 0-5) seven straight times.
Flynn, who was 2-for-15 against Cincinnati and had just one assist with six turnovers against West Virginia, was 10-for-15 as the Orange shot 60.4 percent (32-for-53) and outrebounded the Scarlet Knights 40-24.
Paul Harris finished with 18 points, eight rebounds and five assists, Arinze Onuaku and Rick Jackson each had nine points, and Scoop Jardine had seven assists and six rebounds for the Orange.
Freshman guard Corey Chandler led Rutgers with 16 points and classmate Mike Coburn had 11. JR Inman, who entered the game averaging 14.7 points and 8.1 rebounds, finished with four points and two boards. Jaron Griffin, who had a career-high 23 points in a 64-49 home loss to Louisville on Sunday, finished with seven points.
Both teams combined for just four points in the first 3:19 before the Orange went on an 8-0 run. Flynn hit a hook in the lane and followed with a layup off an inbounds pass to give Syracuse a 10-2 lead at 13:20.
Earl Pettis hit a 3 from the right corner to lead the Scarlet Knights back, and they tied the game at 14-all on a three-point play by Chandler midway through the period.
Then the Orange took control with a 17-2 run over the next 7 minutes. Flynn, who had nine points in the spurt, began it with a 3, Greene scored four points, and Harris finished it with a jumper in the lane to make it 31-16 with 3:55 left in the opening half.
Griffin snapped the skid with a jumper just over a minute later, but Jardine fed Onuaku for a dunk and Harris for a layup before Flynn set up Greene for a reverse dunk as the Orange built a 38-18 lead with 1 minute left.
Rutgers scored twice in the final minute on Inman's dunk and a pullup jumper in the lane at the buzzer by Coburn to cut the lead to 38-22 at halftime.
Syracuse shot 58.6 percent (17-for-29) in the period and outrebounded the Scarlet Knights 19-9, limiting them to just one on the offensive glass.
The Orange didn't let up in the second half and extended the lead to 69-37 on a layup by Flynn at 9:16.
Rutgers, the poorest shooting team in the Big East from beyond the arc at 27.9 percent, went 6-for-19 (31.6 percent).
