Chen began his 2016–2017 season with a gold medal at the 2016 CS Finlandia Trophy, 7.71 points ahead of the silver medalist Patrick Chan of Canada. He then competed at two Grand Prix events. For his Grand Prix series debut at the 2016 Trophée de France in Paris, he cleanly landed a quadruple lutz and triple toe combination jump and a quadruple flip in both his short and long programs. His short program scored 92.85, breaking the American short program record of 90.30 held by Olympic champion Evan Lysacek since the 2010 Winter Olympics. After finishing fourth in France, he returned to Arutyunyan in California. At the 2016 NHK Trophy in Sapporo, Chen placed second behind the reigning Olympic champion Yuzuru Hanyu, qualifying him for the Grand Prix Final (GPF) in Marseille, France.