The collapse lake area due to coal mining in Huaibei shows high biodiversity, but the bacterial community composition and diversity in the lake sediments are still rarely studied. Therefore, based on 16S rRNA high-throughput sequencing and combined with analysis of environmental factors, we comparatively analyzed the bacterial community composition and diversity of surface sediments from East Lake (DH) and South Lake (NH) and Middle Lake (ZH) in the collapse lake area of Huaibei. The bacterial community compositions are significantly different in the sediments among Huaibei collapsed lakes, with DH having the largest number of species, and NH having a higher species diversity. Pseudomonadota is the most abundant phylum in the sediments of DH and NH, while the most abundant phyla in ZH are Bacteroidales, Chloroflexales, Acidobacteriales, and Firmicutes. Anaerolineae (24.05% ± 0.20%) is the most abundant class in the DH sediments, and Gammaproteobacteria (25.94% ± 0.40%) dominates the NH sediments, Bacteroidia (32.12% ± 1.32%) and Clostridia (21.98% ± 0.90%) contribute more than 50% to the bacteria in the sediments of ZH. Redundancy analysis (RDA) shows that pH, TN, and TP are the main environmental factors affecting the bacterial community composition in the sediments of the collapsed lake area. The results reveal the bacterial community composition and biodiversity in the sediments of the Huaibei coal mining collapsed lakes, and provide new insights for the subsequent ecological conservation and restoration of the coal mining collapsed lakes.