The characteristics of macroinvertebrate community structure can effectively reflect the health status of lake ecosystem and the quality of the lake ecological environment. It is of great significance to identify the limiting factors of macroinvertebrate community structure for the maintenance of lake ecosystem health. In this study, the community composition of macroinvertebrate assemblages and their relationships with environmental variables in 13 small lakes within Linhuan Lake was investigated. Self-organizing map, K-means clustering analysis, principal component analysis, pearson correlation analysis, and redundancy analysis were used to analyze the correlation and variability between macroinvertebrates community index and environmental factors. The results showed that the environmental variables (pH, total phosphorus, nitrate, water temperature, dissolved oxygen, conductivity, chemical oxygen demand, and ammonium) had a significant effect on the classification of macroinvertebrate community. Molluscs were significantly negatively correlated with pH and chlorophyll a, while annelids and aquatic insects were significantly positively correlated with chlorophyll a and dissolved oxygen. Species richness and Shannon’s diversity of macroinvertebrates were significantly negatively correlated with total phosphorus while biomass of macroinvertebrates was significantly negatively correlated with pH. High alkalinity characteristics and eutrophication of the lake have a serious impact on the macroinvertebrate community. Human interference and unreasonable industrial and surface runoff from agricultural farms destroy the ecological environment and affect the community structure of macroinvertebrate. Thus, the improvement of the macroinvertebrate’s community structure should be carried out by improving the Lianhuan Lake watershed ecological environment and controlling watershed environmental pollution.