Teenager Andrew Torgashev proved to be the surprise package as he stood third (97.87) and world bronze medallist Vincent Zhou fourth at 94.82 heading into Sunday's free skate.
"I'm thrilled with it," Chen, who had scored 113.42 points at last year's U.S. championships, told NBC Sports.
"I wasn't sure how things would go. Of course I got the flu. Training was a little bit shaky. I wasn't able to get my jumps in. This was the least prepared I have been but I really made good use of the last week."
A victory on Sunday will make him the first American man to win four consecutive titles since Brian Boitano in 1988.
"A skater like I have never seen before," three-time U.S.. champion Johnny Weir, an NBC analyst, said after Chen skated.
Chen said, "Everything felt really calm, really paced throughout the program. I felt I was really in control with that I was doing."
Free dance and pairs free skate were scheduled for later on Saturday.
The top three U.S. finishers qualify for March's world championships in Montreal. (Reporting by Gene Cherry in Salvo, North Carolina, editing by Pritha Sarkar)