Metagenomics was used to analyze the phage community structure in the water and sediment of Huangshui River, Weihe River and Luohe River, and the diversity, host and functional potential of the three tributaries of the Yellow River were compared. The results showed that 99.77% of the unknown vOTUs (viral Operational Taxonomic Units) identified from the metagenome could not be clustered with the NCBI Refseq database, indicating a high degree of species novelty in the phage community. A total of 158 genera belonging to 15 families were detected in three tributaries. The endemic phage genera were the most in Huangshui River and Pbi1virus, Badnavirus, Ea214virus and Gammabaculovirus were detected only in this tributary. The phage community structure of the three tributaries was significantly different and the spatial heterogeneity was greater in the sediment samples. Diversified auxiliary metabolic genes (AMGs) indicated that phages might be involved in the cycling of nitrogen, carbon and phosphorus in Huangshui River, Weihe River and Luohe River, but there was no difference in the distribution of AMGs in the three tributaries. The host range of phage community spanned 18 prokaryotic phyla, mainly including Proteobacteria, Actinobacteriota and Bacteroidota. About 1.8% of the phages might infect hosts across phyla. Phages infecting Planctomycetota were enriched in water and sediments of Luohe River, while Chloroflexota-infected phages were relatively abundant in the sediments of Weihe River. There was a significant correlation between the bacterial and phage community and the consistency was higher in water samples.