The 17-year-old smashed her mark of two minutes 19.25 seconds set in Paris in January 2001 with a time of 2:18.86.
Qi had also broken a World Cup record in the 200 individual medley on Sunday.
Compatriot Luo Xuejuan, third behind Qi in the 200, took the 50 metres breaststroke in 31,03, ahead of Li Wei and Pang Duenyi.
World record holder Anna-Karin Kammerling of Sweden came up short of her own record but managed to win the 50 metres butterfly ahead of China's Zhou Yafei and Martina Moravcova of Slovakia.
Yana Klochkova of Ukraine took the 400 individual medley with a time of 4:33.91, well short of her own world mark of 4:27.83.
In the men's events, Briton James Hickman took first in the 200 individual medley and the 100
In the medley, his time of 1:58.89 edged out Wu Peng, the Chinese teenager who made a stunning showing at the Asian Games, and another compatriot Li Ziqiang.
Hickman outswam Igor Marchenko of Russia and Kaio Almeida of Brazil with a time of 52.20 in the 100 butterfly. The Briton had won the 200 butterfly on Sunday.
Some of the world's top swimmers are not competing in Shanghai, preferring to prepare for the European short-course championships scheduled for December 12-15 in Risa, Germany.
