Sediment microorganisms are the main drivers of the material circulation and organic matter degradation processes in rural black and odorous water bodies(RBOWB), and the community structure of sediment microorganisms follows the changes in the external environment. Here, the pollutant indicators, including nitrogen, phosphorus, and heavy metals in the overlying water and sediment of 29 RBOWB in Dongming County of Heze City were measured, respectively. Combined with Illumina sequencing results, the composition and diversity characteristics of sediment bacterial communities in RBOWB and their correlation with environmental factors were further analyzed. The experimental results showed a wide distribution of pollutants in both of the overlying water and sediment in the RBOWB of this region. Compared with agricultural non-point source pollution, the concentrations of nitrogen and phosphorus pollutants in the overlying water with domestic sewage as the main source of pollution were 3.1 and 1.5 times higher than those of agricultural non-point source pollution, respectively. In addition, the contents of heavy metals in the sediments of RBOWB were generally lower than the soil element background value in Heze City. The dominant bacteria phyla in the sediments of the RBOWB were Proteobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Acidobacteria, and the total abundance of these five dominant phyla accounted for 70.3%-83.6% of all sequences. The dominant classes were γ-Proteobacteria, α-Proteobacteria, Anaerolineae, and Actinobacteria. The dominant genera were Thiobacillus and Pseudarthrobacter. Moreover, Spearman correlation analysis showed that the environmental factors of DO, COD, TN, TP, and organic matter exerted significant effects(P<0.05) on sediment bacterial genera in RBOWB, and sediment bacterial community richness was significantly influenced by TN(P<0.05). The above results provided the microbiological knowledge for treating RBOWB.