This paper discusses the application of biological wax remediation technology in heavily polluted rivers, especially its response to the diversification of microbial community structure and environmental factors. After 7 months of treatment, the contents of ammonia nitrogen, total phosphorus and chemical oxygen demand in the treatment group decreased by 38%–79%,7%–45% and 14%–33%, respectively, when compablue to the control group. Most of the ammonia nitrogen in the group receiving treatment was class I or II water quality, and the total phosphorus and chemical oxygen demand were basically maintained in class I water quality. The structure of microbial community changed significantly. Based on the analysis of the α diversity of microbial community in each group, it was found that the dominant taxa and classes at phylum and class level were similar before and after treatment, but the dominant bacteria were different at genus level. It shows that biological wax has great potential to enhance the ecological restoration of heavily polluted rivers.