In this paper, the upper (0–5 cm ) and bottom ( 5–10 cm ) sediments were collected from healthy and diseased crab ponds in Yangzhong area of Jiangsu Province, and microbial community structures and main affecting factors of the sediments were determined and compared. The results showed that pH (7.77) and total potassium (1.78 g/kg) in diseased sediment were significantly lower than those in the healthy one (7.91, 1.95 g/kg), while total water-soluble salt (1.50 g/kg) was significantly higher than that in the healthy one (1.05 g/kg). Microbial diversity (Shannon index) was significantly higher in 5–10 cm than that in 0–5 cm of healthy sediment (P<0.05), while microbial richness (ACE and Chao indexes) and diversity (Shannon index) were significantly higher in 5–10 cm than in 0–5 cm of diseased sediment (P<0.05). The dominant bacteria in the sediments of the two groups were Proteobacteria, Chloroflexi and Acidobacteriota. There were many different bacteria including Bacillus in healthy and diseased pond sediments. The correlation analysis showed that total nitrogen was the main environmental factor affecting microbial community of crab pond sediment. In addition, water-soluble salts, calcium carbonate and total sulfur were the environmental factors determining microbial community in healthy pond sediment, while organic matter and pH were the environmental factors for the diseased one. The results of this study can provide a theoretical reference for the microecological regulation of crab ponds farming.