Abbott, 26, earned 183.35 points during the free skate, topping the score of 157.93 posted by Adam Rippon.
Abbott skated last Sunday after placing first in Friday's short program. He earned a total of 273.58 points, while Rippon finished in second with 240.87. Ross Miner had been fourth after the short program, but finished in third (230.32) with a strong performance (151.42 points) in the free skate.
Abbott won his other national titles in 2009 and 2010.
Also on Sunday, Caydee Denney and John Coughlin clinched the title in the pairs competition by winning the free skate. They earned 128.82 points in the free skate and finished with 189.70.
Mary Beth Marley and Rockne Brubaker had been first after the short program, but earned 120.27 points for their free skate and ended with 186.07. Amanda Evora and Mark Ladwig were third with 178.98 total points.