In order to study the characteristics of plankton community structure, diversity and water quality status in the Chongqing Section of the Yangtze River Basin (hereafter referred to as the Chongqing Section), and to assess the health status of water ecology in the region, 14 sampling transects were set up in the Chongqing Section from May to June 2022, and the plankton in each sampling transect was surveyed and analyzed, and the plankton diversity index was applied to assess the water quality pollution. The degree of water pollution was assessed using the plankton diversity index. The results showed that: 1) A total of 132 species of phytoplankton from 63 genera in 8 phyla were identified, among which the diatom phylum (Bacillariophyta) had the highest number of species, and its density and biomass were also large; the number of species of the green alga phylum (Chlorophyta) and cyanobacteria phylum (Cyanophyta) was also high; and the phytoplankton diversity indices corresponded to the degree of water pollution ranging from clean to mildly polluted. The phytoplankton diversity index corresponded to water pollution levels ranging from clean to mild. 2) A total of 56 species of zooplankton from 5 phylums and 31 genera were identified, among which Rotifer had the highest number of species, accounting for 50% of the total number of zooplankton species; Cladocerans and Copepods had high densities and high biomasses; and the zooplankton diversity index corresponded to the degree of water pollution ranging from mild to moderate pollution. The results suggest that the phytoplankton in the Chongqing Section is dominated by diatoms, and the zooplankton is dominated by Rotifers, Cladocerans and Copepods; the phytoplankton is more abundant than the zooplankton; the overall water quality in the Chongqing Section ranges from clean to moderately polluted, and the management and protection of the water ecosystems in the section need to be strengthened and emphasized.