Less is known about the interaction of viruses with their prokaryotic host in the gut of wild animal. Here we used fecal DNA metagenomic data (n = 24) from black-necked cranes during the wintering period for virus characterization. The results were found to be consistent with the trend of bacterial community changes, and the black-necked crane gut viruses community structure was conservative during the wintering period. A total of 280 vOTUs (6 complete, 3 HQ, 2 MQ and 269 LQ) were obtained and life history predictions identified 207 virulent viruses. 269 LQ vOTUs contained at least 10 viral genes, hence several of these viruses may be too distinct from viral species in the CheckV database to properly estimate their completeness. Meanwhile, gene-sharing network analysis revealed that the gut viruses of black-necked crane formed 32 unique viral clusters (VCs). Virus taxonomic assignment has revealed that Azeredovirinae is the most abundant family during the wintering period of black-necked cranes. Furthermore. Black-necked crane gut viruses have a complex relationship with their prokaryotic hosts, and virus-encoded auxiliary metabolic genes (AMGs) enhance the potential of infecting bacteria for chitin degradation, methionine and tetrahydrofolate (THF) metabolism. These results imply the presence of a large number of novel viruses in the intestinal tract of black-necked cranes, which may further affect birds by regulating prokaryotic bacterial metabolism including lyse prokaryotic host cells and encodes AMGs related to the degradation of complex carbohydrates and amino acid metabolism.