Abstract: From 2016 to 2018, we seasonally collected fish and monitored the environmental factors at the six sites from Guiping to Zhaoqing in the West River, the main stream of the Pearl River. In total, we collected 99 species belonging to 12 Orders and 29 Families. The species number collected for each sampling ranged from 10 to 45, while the Shannon-Weiner index ranged from 0.90 to 2.93, and the evenness index ranged from 0.30 to 0.89. The species variation was agreed with patterns of seasonal turnover and spatial turnover. As revealed by the index of relative importance, Cirrhinus molitorella, Megalobrama terminalis and Squaliobarbus curriculus were the most dominant fish species. The permutational multivariate analysis of variance indicates that the fish community structure varied significantly among seasons and sites. The significant difference between summer and winter was mainly caused by the weight percentage variation (W%) of Cyprinus carpio, C. molitorella, M. terminalis and S. curriculus. The significant difference between Guiping and lower reaches of Wuzhou and Zhaoqing was mainly caused by the number percentage (N%) variation of C. molitorella, M. terminalis and Squalidus argentatus, and W% variation of C. molitorella, M. terminalis, C. carpio, Hypophthalmichthys molitrix and Oreochromis niloticus. Redundancy analysis explains 49.92% variation of fish N% and 49.61% of fish W%; the most important influencing variables are distance to estuary, water temperature, water transparency and runoff; C. molitorella distributes in water of low transparency and high temperature; M. terminalis and H. molitrix distributes in lower reach; S. curriculus distributes in middle and upper reach; C. carpio distributes in water of high transparency and low temperature.