Abstract: In order to investigate the diversity, function and potential harm of viral community in the reservoirs at the middle part of the Northern Tianshan Mountains, Santunbei Reservoir (STW), Bayi Reservoir (BYW) and Moguhu Reservoir (MGW) were selected as typical reservoirs. Concentrated virus particles were obtained from the reservoir water samples by FeCl₃ flocculation and enriched by polyethylene glycol (PEG). The diversity and function of the viruses were then analyzed by viral metagenomics, and the genetic sequences of pathogens were analyzed. The results showed that: (1) From the typical reservoirs of STW, BYW and MGW at the middle part of Northern Tianshan Mountain, 36, 784, 178, 32, 434, 254 and 30, 537, 928 viral sequences were obtained, and 15, 400, 11, 894 and 30, 771 contigs were formed, respectively. (2) The viruses from the reservoirs belonged to 9 families and 26 species, among which 3 families belonging to Caudovirales were found to be the dominant viruses at the virus family level. Myoviridae showed a highly relative abundance in BYW and MGW, while Siphoviridae showed relative high abundance in STW. At the species level, Streptomyces phages, Microcystis phages and Erwinia phages exhibited relative high abundance in STW, BYS and MGW, respectively. (3) Viral gene analysis indicated that the genes related to capsid protein and tail protein as well as viral replication and assembly showed relatively a high abundance. (4) Several pathogens of plants and animals were found in the reservoirs, among which enterovirus showed relatively abundant in MGW, and the VP1 gene sequence of Coxsackievirus A10 (CV-A10) obtained was consistent with the original Kowalik strain. In summary, bacteriophages were all the dominant viruses in the reservoirs, and the virus replicated actively. The composition of the viral communities in different reservoirs was different, which could be related to the surrounding environment and human activities. The results of this study indicate that the presence of pathogenic viruses (CV-A10, for instance) in the reservoirs could be a potential risk to public health.