Abstract: The community structure and influencing factors of macroinvertebrate in the Hongze Lake were systematically studied in April and September 2018. The results showed that 37 species of macroinvertebrate were identified, belonging to 4 families, 8 classes, 13 orders and 19 families. The dominant species were Limnodrilus hoffmeisteri, Gammarus sp., Nephtys oligobranchia, Microchironomus tener, Corbicula fluminea, with dominances were 0.108, 0.068, 0.054, 0.037 and 0.020, respectively. Species richness, Margalef diversity index and Shannon index were significantly higher in April than in September. Non-matric multidimentional scaling ordination (NMDS) and PerMANOVA confirmed the difference of benthic community during the two surveys. Indicator species analysis showed that Harnischia fuscimana, Microchironomus tener, Teneridrilus mastix, Laonome sp., Branchiura sowerbyi were the key species responsible for the difference of macroinvertebrate community between the two surveys. Distance-based redundancy analysis (dbRDA) was used to identify the key factors affecting macroinvertebrate community structure; and the results showed that the community structure was mainly affected by conductance, water temperature, chlorophyll a and silicate in the April; while, the key factors affecting macroinvertebrate community in September were phosphate, water depth and dissolved oxygen. This study lays a data and theoretical foundation for further research on macroinvertebrate ecology of the Hongze Lake and evaluation of the impact of inter-basin water transfer on freshwater ecosystem.