Hanyu recorded 95.07 for his display to take the early lead in the event, with his compatriot Takahiko Kozuka second and America's Jeremy Abbott third.
The world record display was the undisputed highlight of the day, beating the previous record of 94 points held by Daisuke Takahashi.
"Ninety-five is an extremely high score and I wasn't expecting it," Hanyu said.
"I want to concentrate on the free skate now. This is only part of the event and I want to control my thoughts until the very end."
In the pairs, Tatiana Volosozhar and Maxim Trankov of Russia topped the rankings after the short programme with a score of 65.78 points, ahead of Olympic silver medallists Qing Pang and Jian Tong of China on 61.96. Reigning US champions Caydee Denney and John Coughlin sit in third place with 60.75.
"We have to think about this because we had the same problem at the World Championships last year," Trankov said. "We're scared of our short program, we're very nervous. We never feel this way about our free skate."
Men's short programme results:
1. Yuzuru HANYU JPN 95.07
2. Takahiko KOZUKA JPN 85.32
3. Jeremy ABBOTT USA 77.71
4. Tatsuki MACHIDA JPN 75.78
5. Konstantin MENSHOV RUS 73.32
6. Michal BREZINA CZE 69.26
7. Armin MAHBANOOZADEH USA 68.27
8. Alexander MAJOROV SWE 60.48
9. Tomas VERNER CZE 58.79
10. Douglas RAZZANO USA 57.06
Pairs short programme results:
1. Tatiana VOLOSOZHAR / Maxim TRANKOV RUS 65.78
2. Qing PANG / Jian TONG CHN 61.96
3. Caydee DENNEY / John COUGHLIN USA 60.75
4. Vanessa JAMES / Morgan CIPRES FRA 55.76
5. Marissa CASTELLI / Simon SHNAPIR USA 55.67
6. Danielle MONTALBANO / Evgeni KRASNOPOLSKI ISR 40.66
7. Gretchen DONLAN / Andrew SPEROFF USA 40.54