Abstract: The index of biotic integrity (IBI) is an important and widely used indicator for the evaluation of river ecosystem health. However, there are few studies on the construction of IBI evaluation criteria based on the use of decomposer microbial communities in water. The evaluation of the ecosystem health of urban rivers in Beijing was carried out, and the evaluation process and criteria construction method of the microbial index of biotic integrity (M-IBI) were explored. Based on the high-throughput sequencing information of microbial Illumina in the sediments, the key environmental factors were screened (water quality indicators TN, TP, NH₃-N, NO₃-N and NO₂-N), and candidate biological parameters were determined. According to the results of discriminant analysis, six indexes were determined, including Shannon index, relative abundance of Bacteroidota, relative abundance of Chloroflexi, relative abundance of Cyanobacteria, relative abundances of COD_Cr tolerance genus and relative abundances of ammonia nitrogen clean genus. The standardized formula of parameters and the health evaluation standards were put forward. The evaluation results showed that each sampling point of the Yongding River supplied by natural water was evaluated as healthy state. Among the other three rivers, supplied by the effluent of the urban reclaimed water plant, four sampling points of the Qinghe River were evaluated as healthy to sub-healthy state, five sampling points of the Liangshui River were evaluated as healthy to general state, and four sampling points of the Dalong River were evaluated as sub-health to general state. M-IBI could effectively distinguish the damaged points of different degrees and give a reasonable evaluation of the health status of the urban river ecosystem.