Based on fish community monitoring data of 10 sites and water environment monitoring data of 33 sites in the Taihu Lake from 2016 to 2020, the fish community structure and diversity were investigated, as well as their relationship with main water environment factors. A total of 55 fish species were collected in 2020, and the dominant species were Coilia nasus, Carassius auratus and Cyprinus carpio,of which the index of relative importance were 9 219.28, 1698.78 and 1 075.27 respectively. Besides, the proportion of 87.9% fish full length <200 mm, and the proportion of 88.2% fish mass body <50 g. A total of 67 fish species have been collected since 2016, and fish community structure changed greatly although the water quality remains stable. The results showed that there was no significant relationship between fish community diversity index and main water environmental factors and the water discharge of Taihu Lake and the artificial propagation and release were the key factors. Refined fishing program and the artificial propagation and release program of Chinese silver carps and bighead carps should be established based on the water environment situation of Taihu Lake, in order to restore the fish community structure and give play to the potential of the Chinese silver carps and bighead carps in controlling algal bloom.