Abstract: Viruses are widely distributed in the natural environment. With the rapid development of high-throughput sequencing technology, more and more studies on the viral genetic diversity have been reported, whereas relatively few on plateau wetland. Viral metagenomics were used to study the population structure and viral genetic diversity in Napahai plateau wetland. Viral sequences were obtained, of which DNA viruses accounted for 99.4%（phages accounting for 47.95%） and RNA viruses accounted for 0.6%. It showed that the dominant virus families were Siphoviridae, Myoviridae, Genomoviridae, Herpesviridae, Phycodnaviridae, and Mimiviridae. The dominant virus familys were related to environmental factors, such as total nitrogen, chlorophyll a and zinc, and was unevenly distributed geographically. Phylogenetic analysis of algae viruses showed that six known algae DNA viruses genera were found in Napahai plateau wetland. The study on virus population abundance, genome function analysis, distribution difference and correlation with environmental factors in Napahai plateau wetland would provide scientific basis for understanding the viral population structure and further clarifying the viral function in the wetland ecosystem.