Plankton, as an important part of the food chain in the river ecosystem, is sensitive to changes in the environment. To investigate the influence of plankton community structure on the aquatic ecosystem and further verify the applicability of biomanipulation, the midstream of the Jialing River was selected as the study area. A total of 149 species (varieties) from 7 phyla, 18 orders, 34 families, and 72 genera were identified for phytoplankton. A total of 48 species were found for zooplankton. The mean density of phytoplankton was 2.09 × 106 cells/L, and the mean density of zooplankton was 27.1 ind./L. Moreover, the mean values of the Shannon–Wiener diversity index (H′), Pielou homogeneity index (J′), and Margalef abundance index (D) for phytoplankton were 3.17, 0.76, and 4.47, respectively. The mean values of the Shannon–Wiener diversity index (H′), Pielou homogeneity index (J′), and Margalef abundance index (D) for zooplankton were 2.64, 0.92, and 5.07, respectively. Based on the diversity indices, the water quality was evaluated as oligo pollution to β-medium pollution level. Redundancy analysis (RDA) was used to explore the relationship between dominant plankton species and environmental factors. The RDA results show that the main environmental factors affecting the community structure of phytoplankton and zooplankton were water temperature (WT), electrical conductivity (EC), pH, total phosphorus (TP), and transparency (Secchi depth; SD). There were 17 functional groups in phytoplankton, which are X1, S1, Y, Y2, and so on. In zooplankton, there were six functional groups, which are Pmsl, Prsu, Pfif, Pmip, Lrsf and Lmic. Many articles have demonstrated the feasibility of using biological manipulation to control algae. The number of piscivorous fish in the midstream of the Jialing River had increased, and phytoplankton density in this survey was significantly decreased. The results show that traditional biomanipulation can be applied to this region, which can provide better scientific support for the future management of the aquatic environment in the Jialing River basin.