Lake Chaohu, as the fifth largest Chinese freshwater lake, is one of the key areas for water pollution prevention in China. It plays a crucial role in supporting ecological civilization development in Anhui Province and promoting Yangtze River protection. The rapid socio-economic development in the Lake Chaohu Basin has exerted significant pressure on the lake, resulting in water quality deterioration and frequent cyanobacteria algae blooms. In the past ten years, despite the improvement in the water quality owing to comprehensive management efforts, eutrophication remained a critical issue, and knowledge about the long-term changes in aquatic biological community structures was still limited, especially for benthic macrozoobenthos. This study combined field survey and historical records to obtain data on benthic fauna and environmental factors from five different periods since 1980. Using principal component analysis (PCA), canonical correspondence analysis (CCA), the study explored the changes in benthic macrozoobenthos density, community structure, and dominant groups over the past 40 years in Lake Chaohu. The results showed that from 1980 to 2022, a total of 77 species (genera) from 3 phyla and 6 classes of benthic fauna were recorded, with significant changes in abundance of entire community and different taxonomic groups. The dominant species have experienced a transition from being primarily composed of cleaner mollusks to a gradual shift towards pollution-tolerant families such as midges and oligochaetes, followed by a slow recovery of cleaner species. Specific changes are as follows: in 1980-1981, species diversity was high, with mollusks being dominant; in 2002-2003, eutrophication intensified, and the benthic community rapidly degraded, with pollution-tolerant oligochaetes and chironomids larvae dominated, with a relative abundance of 96.1%; in 2008-2009, the relative abundance of oligochaetes and chironomid larvae decreased to 87%; in 2013-2014, the relative abundance of Chironomidae increased, but the relative abundance of Oligochaeta dropped from 55.1% to 24.1%, with the two species collectively accounting for 96.5%; in 2022, the abundance of benthic fauna dropped to the lowest historical level (278 ind./m2), the relative abundance of Oligochaeta fell to 6.9%, and the number of bivalve mollusks increased from two in 2013-2014 to five, with the national protected species, theNovaculina chinensisbeing found at nine sites with an occurrence of 30%, indicating a recovery of biodiversity. Over the past 40 years, total nitrogen, chlorophyll-a , dissolved oxygen, water depth, sediment total nitrogen, and wind speed have been the main environmental factors influencing the succession of the benthic macrozoobenthos community.