The 26-year-old clocked 4:18.51, way ahead of second-placed Hong Kong’s Sze Hang Yu’s time of 4:25.15 at the Bukit Jalil Aquatic Centre.
Angela Chieng Chui Fei of Sarawak took the bronze in 4:29.13.
For Cai Lin, it was a sweet victory as she was beaten to the gold by Hang Yu in the 200m freestyle on Friday.
“I am satisfied with my performance today as I was able to improve my time,” said Cai Lin.
It was her third medal in the championships, having won the 400m individual medley gold on Thursday.
Cai Lin will be looking to add one more medal to her collection today when she competes in the 800m freestyle.