Two-time Olympic champion Hanyu opened his performance with a quadruple loop and eventually collected a level four for his spins and footwork, racking up 305.5 points overall for his eighth Grand Prix gold medal.
"For now, I'm happy that I was able to get through, leading up the free program, stayed healthy, had no pain and no injuries," Hanyu said.
France's Kevin Aymoz took the silver medal, 55 points behind, with Canadian Roman Sadovsky finishing third.
In the women's event, favourite Alena Kostornaia of Russia stormed to victory for her second Grand Prix gold, with 240 points overall.
Rika Kihira of Japan was in silver on 231.84, Olympic champion Alina Zagitova of Russia in bronze.
In ice-dance pairs, four-time ISU world champions Gabriella Papadakis and Guillaume Cizeron of France set new highest scores on their way to gold.