Microplastics have been of great concern in recent years due to bioaccumulation and their toxic effects on organisms. However, few studies have focused on microplastics in the natural river ecosystem and the relationship between microplastics and microbes. Therefore, to understand the concentration and characteristics of microplastics and explore the impact of microplastics on the microbial community, sediment samples were collected from the Huangjinxia Reservoir, which is the water source of a water diversion project in western China. Results showed that the concentration of microplastics in the study area ranged from 233.33 ± 70.24 items·kg-1 to 870 ± 238.12 items·kg-1, with an average of 558.10 ± 291.45 items·kg-1. After clustering the sediments according to the microplastic concentration, there was a significant difference in the Chao1 index of microbial community between groups, indicating that microplastics might have affected microbial diversity of the sediments. Additionally, Anosim, MRPP, and Amova analyses indicated that microplastics might have an impact on the structure and composition of microbial communities. Moreover, function prediction assays suggested that microplastics might have differential impacts on various microbial community functions. To our knowledge, this is the first study to explore the impact of microplastics on microbes in sediments of a natural river ecosystem, providing a basis for further study of the interaction between microplastics and microbes in similar habitats.