Taking Ceratophyllum demersum, Elodea nuttallii, Nuphar pumilum and Trapa natans as the study objects, the distribution of epiphytic microbes and bacterial community structure of different aquatic macrophytes were probed by scanning electron microscopy, fluorescence microscopy and 16S rRNA high-throughput sequencing technology. The results showed that the density of epiphytic algae was higher on the submerged plants than those on the floating plants. And the composition of epiphytic algae was significantly different from that of surrounding water. The community structure on the roots of floating plants(Nuphar pumilum, Trapa natans)was significantly different from those attached to the leaves. The dominant phyla of bacteria attached to the surface of four aquatic plants were Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Acidobacteria and Verrucomicrobia, which had the function of purifying polluted water. There were a large number of epiphytic microorganisms on two types of plants, and there were some differences in the dominant species between different aquatic macrophytes and between different organs on the same plants.