This study was conducted in April 2022 (spring), June 2023 (summer), October 2023 (autumn), and January 2024 (winter) to understand the relationship between fish community structure and diversity as well as environmental factors in the Henan section of the Yellow River (Hongnongjianhekou, Qinglongjianhekou, Nancun, Shuangmacun, Tongshuling, Yiluohekou, Liuyuankou, Naoli, Tianranwenyanqukou, and Jindihekou). Using the obtained data, fish community structural characteristics, spatial and temporal distribution patterns, and their relationship with environmental factors were analyzed. A total of 16556 individuals belonging to 47 species, 40 genera, 15 families, and five orders were collected, among which, there was one species of fish under state secondary protection and five exotic fish species, accounting for 2.1% and 10.6% of the total species, respectively. According to the index of relative importance (IRI), the dominant fish species were small fishes, such as Parabramis pekinensis, Rhinogobius giurinus, Cyprinus carpio, Pseudobrama simoni, Hypophthalmichthys molitrix, and Hemiculter leucisculus. The average Margalef richness, Pielou evenness and Shannon-Wiener diversity were 3.01±0.68, 0.56±0.16, 2.49±0.77, respectively. The abundance/biomass comparison curve showed that the fish communities in Nancun, Tongshuling, Naoli, and Jindihekou were relatively stable, whereas those in Hongnongjianhekou, Qinglongjianhekou, Shuangmacun, Yiluohekou, Liuyuankou, and Tianranwenyanqukou were seriously disturbed. Cluster and non-metric multidimensional scale ranking (NMDS) analyses showed that the fish communities in Henan section of the Yellow River could be divided into three groups: those in Hongnongjianhekou and Qinglongjianhekou belong to one group; those in Naoli, Tianranwenyanqukou, Jindihekou, Nancun, Yiluohekou, and Liuyuankou belong to one group; and those in Shuangmacun and Tongshuling belong to one group. RDA analysis showed that permanganate (CODMn) and suspended substance (SS) were the main environmental factors affecting the differences of fish community structure in the Henan section of the Yellow River. These results show that, compared with the historical data, the fish community structure in the southern section of the Yellow River has obviously changed, alien species have increased, indigenous fish have decreased, and individual fish tend to be smaller and younger.