Sediment microorganisms are the main source of sediment metabolism in urban rivers, which ultimately determine the ecological status of the rivers. In this paper, to analyze the effect of different ecological treatments on sediment microbial community, we established artificial mesocosms to mimic sediment status of the black-stinking river with different ecological treatments as calcium nitrate, bio-energizer addition, and submerged macrophytes transplantation. Illumina Miseq sequencing was applied to reveal the bacteria community variations of all treated and untreated sediments. The results showed that in the overlying water, the total nitrogen (TN) content of calcium nitrate addition group was significantly higher than that in the control group, dissolved oxygen concentration in the bio-energizer addition group was significantly higher than that in the control group. In the sediment, the oxidation reduction potential (ORP) values of all the treatment groups were significantly higher than those in the control group; TN content of calcium nitrate addition group and submerged macrophytes transplantation group were both significantly lower than those in the control group, which indicate the improvement of sediment status of treatment group. Bacterial communities were also varied in treatment group, and showed diverse variations with different treatments. The Sobs and Chao 1 microbial diversity indices in the bio-energizer addition group were both significantly higher than those in the control group and calcium nitrate addition group; the Shannon and PD diversity indices for microbes in the bio-energizer addition sediment were both significantly higher than those in calcium nitrate addition group. All sediment microbial communities were dominated by Proteobacteria (Deltaproteobacteria, Betaproteobacteria, Gammaproteobacteria), Chloroflexi, Firmicutes, Bacteroidetes and Spirochaetae phyla. Nonmetric multidimensional scaling analysis showed that the addition of calcium nitrate and bio-energizer can significantly alter the composition of bacterial community structure. Uncultured_Anaerolineaceae, Ferribacterium and uncultured_Xanthomonadales_Incertaeae_Sedis were the main genus causing variations in the bacterial community. Redundancy analysis indicated that the change of sediment ORP is a key environmental factor driving the variation of bacterial community structure.