Abstract: In order to clarify the microbial community structure, function and influencing factors of ecological restoration rivers, the Qingyi River in Xuchang City was taken as an example, and high-throughput sequencing methods were used to study the influence of ecological restoration measures on the microbial community structure of river water and sediment, and then the purification effect of carbon, nitrogen and sulfur functional bacteria in ecological restoration measures and the distribution of waterborne pathogenic bacteria were analyzed. The results showed that: In the river sections with less human interference, the near-natural riverbank had a good interception effect on land-source pollution, and the interception and oxygenation capacity of ecological filter dams could help the river to remove chemical oxygen demand (COD). The water quality of the urban river section was greatly affected by human activities, and the purification effect of ecological restoration measures was not obvious. In the suburban river section, human interference was less, the river's self-purification capacity was improved, and the total phosphorus (TP) and ammonia nitrogen (NH₄ ⁺-N) indicators gradually returned to the original level. The microbial diversity and richness of the Qingyi River sediment were higher than that of the overlying water, and Proteobacteria was the dominant species in sediment and water. The relative abundance of Cyanobacteria, which participated in the nitrogen cycle, reached 4.7%, indicating that the Qingyi River still had eutrophic river sections. The most abundant pathogenic bacteria in the Qingyi River water was Acinetobacter, while the most abundant pathogenic bacteria in sediment were Clostridium, Flavobacterium and Bacteroidetes, among which Bacteroidetes was the most abundant in the urban section. Spearman correlation analysis showed that there was a significant correlation between microbial diversity in water and temperature (T), pH, COD (P<0.05). The main factors affecting the microbial community structure in the suburban sediment were NH₄ ⁺-N, total nitrogen (TN) and TP. The results showed that the abundance and diversity of microbes in the urban section of the ecologically restored river were high and the risk of pathogenicity was high; the abundance of carbon, nitrogen and sulfur functional bacteria in the suburban section was high, and it was the main place for material cycling.