"I made a little bobble on my (triple) axel, but this is something I will try to focus on for tomorrow," Chen said after an otherwise near perfect routine that also included a quad Lutz-triple toe combination and a quad flip.
Utah-born Chen, 18, is the only skater with five different types of quad jumps, all of which he might try in Saturday's free skate.
Though he has yet to lock up a spot on the American team for the Pyeongchang Winter Games in February, Chen is expected to be one of the favourites based on his form this season.
Canadian double world champions Meagan Duhamel and Eric Radford took the lead in the pairs short programme ahead of Chinese duo Xiaoyu Yu and Hao Zhang.
However, both pairs expressed dissatisfaction with their performances.
"There are aspects ... that I’m really proud of and aspects that I am frustrated with," Radford said.
"I am really proud of how we felt the programme and stayed in the moment. I am frustrated with our levels. We lost levels on elements that we usually don’t lose points on. We don’t want to make those mistakes heading into the rest of the season."
Zhang was similarly self-critical.
"Compared to Cup of China, I felt we had less energy," Zhang said, referring to the event three weeks ago where he and Yu finished second.
"I was a bit tired in practice the first few days and had problems with the solo jump, but today in competition it was fine."
With 75.37 points, Duhamel and Eric Radford headed Yu and Zhang (73.67 points), with German pair Aliona Savchenko and Bruno Massot third on 72.55 points.
Skate America is the sixth and last regular event in the ISU Grand Prix series before the final in Japan next month.
(Reporting by Andrew Both in Tokyo; Editing by Amlan Chakraborty)
