Mitten crab aquaculture is prevalent in China, however, knowledge about the threat of cyanobacteria in mitten crab aquaculture-impacted water bodies is limited. Here, seasonal variations of cyanobacteria and their relationships with environmental factors were investigated for Lake Guchenghu area. Results suggested the changes of cyanobacteria community in crab ponds distinguished from the adjacent lake. In the lake, cyanobacterial biomass (3.86 mg/L, 34.6% of the total phytoplankton) was the highest in autumn with the dominance of Oscillatoria, Aphanocapsa and Pesudanabaena. By contrast, in crab ponds, cyanobacteria (46.80 mg/L, 97.2% of the total phytoplankton biomass) were the most abundant in summer when Pesudanabaena and Raphidiopsis were the dominant species. Of particular note was that obviously higher abundance of filamentous and potentially harmful species (e.g., Raphidiopsis raciborskii and Dolichospermum circinale) were observed in ponds compared to the lake. Specifically, water depth (WD), permanganate index (COD_Mn), total phosphorus (TP), N:P ratio, and ${\mathrm{NO}}_2$ ⁻-N were the key environmental variables affected cyanobacteria composition. For crab ponds, N:P ratio, water temperature (WT) and TP were the potential environmental drivers of cyanobacteria development. This study highlighted the fact that mitten crab culture had non-negligible influences on the cyanobacteria community and additional attention should be paid to the cyanobacteria dynamics in mitten crab culture-impacted water bodies, especially for those potentially harmful species.