Submerged plants, such as the Hydrilla verticillata, Vallisneria natans , Elodea nuttallii and Potamogeton crispus L , were selected as the research objects. This study used the scanning electron microscopy, fluorescence microscopy and 16S rRNA high-throughput sequencing technology to explore the bacterial community structure and influencing factors attached to the leaf surface of submerged plants in different habitats. The results show that the composition of algae attached to the leaf surface of submerged plants is significantly different from that in the environmental water body. Different submerged plants have different density of microorganisms on the leaf surface, and the density of microorganisms attached to the surface of lake samples are lower than the river samples. α-Proteobacteria, β-Proteobacteria and γ-Proteobacteria are the main bacterial classes in the biofilm on the leaves of submerged plants. These classes have the function of degrading pollutants and purifying water bodies. Redundant analysis shows that the concentration of nutrients in the water body has a great influence on the microbial community structure on the leaf surface of submerged plants.