She clocked one minute and 10.07 seconds in the S14 race, more than three seconds faster than Fang Zheng of Hubei.
Fellow Hong Kong swimmer Lau Chiu-yee took bronze medal.
Chan has so far won two golds and two silvers at this year’s Games, and she is due to compete in the 100m butterfly on Sunday.
In the women’s 100m backstroke S7 race, Ng Cheuk-yan took silver in a little under one minute 33 seconds.
In the men’s 100m backstroke S14, Hui Ka-chung claimed silver after finishing in one minute 2.55 seconds.
The race was won by Zhejiang’s Liu Jiaming, who led from start to finish and set a new national record of 58.66 seconds.
Hui said he did better than expected.
“I used all my energy in this race. I made sure to swim based on my own instincts and avoided the distractions of others,” he said afterwards.
“I want to thank my family for their support and also my coach for all his help.”