To explore the relationship between plankton community structure, functional group characteristics and environmental factors in the Hongan River within the Xiushan section of Chongqing. In June 2025, plankton sampling was conducted at 12 sampling sites along the main stream and tributaries of the Hongan River, and analyses were conducted from both taxonomic and functional group, which relevant environmental factors were also measured. The results showed that: 1) A total of 334 species of phytoplankton belonging to 8 phyla were identified, with Bacillariophyta being absolutely dominant (52.10%). The phytoplankton were divided into 24 functional groups, with littoral benthic diatoms being the dominant functional group. For zooplankton, 84 species belonging to 4 categories were identified, with rotifers accounting for the highest proportion (48.81%); they were classified into 6 functional groups, with protozoan filter-feeders being the dominant one. 2) In terms of spatial distribution, the plankton community in the main stream had high diversity and strong stability, showing the characteristics of multi-functional group coexistence; while the plankton community in the tributaries had low diversity and presented a simplified pollution-tolerant structure. 3) Among the key environmental driving factors, TN, TP, NH3-N, DO, and Chla jointly shaped the community differences between the main stream and tributaries, and altitude further amplified the local community differentiation. This study reveals the adaptive response mechanism of plankton under the environmental stress gradient, and provides key scientific basis for the aquatic ecological protection and the differentiated management and control of the main stream and tributaries in the Hongan River.