With a quadruple Salchow and a quad toe-loop triple toe-loop combination, Hanyu broke his own record points haul of 110.53 in 2018 to score 111.82, beating China's Jin Boyang by a margin of 15.99 points while American Jason Brown finished third.
Hanyu, who had decided to revert to the routine that helped him win gold at the PyeongChang Olympics in 2018, skated to Frederic Chopin's "Ballade No. 1" and set the crowd abuzz when he landed his opening quad Salchow.
"I think I skated with elegance... and today's performance was the most perfect performance I've ever done," Hanyu, 25, said. "Also, I tried to express my music deeply with my feeling and I could jump higher and with more perfection.
"Actually, I set as a goal a score higher than 110 for myself. I grew confident during the performance because I felt so good while I skated."
In the Ice Dance event, the American pair of Madison Chock and Evan Bates won the first title up for grabs, defending their crown after they were the last couple to step out on to the ice.
Despite a scare when Chock slipped during a transition, they recovered and finished with a total score of 213.8 points to move up to first, ahead of Canada's Piper Gilles and Paul Poirier who took the silver medal.
"I scared myself. Maybe I stepped on something," Chock said about her fall. "It was out of the blue. I was trying to catch myself... It feels so good, I'm so happy. This is a really special event for us. We love Four Continents."
Bates said their recovery was a "testament to how well-trained" they were.
"The jolt kind of took some energy away from us," he said. "Just coming off our national championships we were just fighting out there to put together the best performance we could and we're just so grateful that we were able to do enough."
The Four Continents championships continue over the weekend with the free skating segment. The Pairs and Ladies Free Skating events will be held on Saturday. (Reporting by Rohith Nair in Bengaluru; Editing by Ken Ferris)