The Ovis ammon polii, an endangered species, has been mainly studied for its external morphological characteristics, geographical distribution, population size, habitat selection, Conservation biology, as well as its evolutionary relationship with sheep. However, research on its gut microbial has been relatively limited. The gut microbiota is critical for animal nutrition metabolism and health. This microbial community, shaped by long-term symbiosis and co-evolution between the host and microorganisms, has become an essential component of the host’s physiological functions. The Pamir Plateau, situated in the heart of the Eurasian continent and extending eastward to the western part of Xinjiang, China, is characterized by an arid climate due to the blocking of moist air currents from the west by high mountains. This results in perennial drought and scarce rainfall, particularly in winter when vegetation withers and biomass significantly decreases. Understanding the role of gut microbiota structural changes under different seasonal conditions in the health and nutrition metabolism of Ovis ammon polii is therefore of significant importance. In this study, we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial communities in fresh fecal samples of Ovis ammon polii collected in April (spring ), July (summer ), and January of the following year (winter ). The results revealed significant differences in the diversity and composition of gut microbiota among the different seasons (P<0.05 ). Specifically, the alpha diversity index of the gut microbiota in Ovis ammon polii was significantly higher in spring and winter compared to summer (P<0.05 ). Analysis of the gut microbial taxa showed that in the spring and winter seasons, the relative abundance of Firmicutes, Verrucomicrobiota, UCG-005, Akkermansia, Christensenellaceae R-7 group, Monoglobus, and Ruminococcus was significantly higher compared to summer (P＜0.05 ). Most of these taxa are associated with cellulose degradation, and such variations likely facilitate the adaptation of Ovis ammon polii to seasons with food scarcity. Conversely, the relative abundance of Proteobacteria, Actinobacteriota, Acinetobacter, and Arthrobacter was significantly lower compared to summer (P＜0.05 ). Additionally, the functional abundance of gut bacteria in the spring-winter group was significantly higher than that in the summer group (P＜0.05 ), with functional genes primarily enriched in carbohydrate metabolism pathways. Differential analysis of glycoside hydrolase enrichment across seasons indicated that the abundance of enzymes related to plant cellulose degradation in the gut microbiota of Ovis ammon polii was significantly lower in summer compared to spring and winter, while the abundance of enzymes related to the breakdown of starch, galactose, and maltose was significantly higher in summer compared to spring and winter. In conclusion, the composition, structure, and functional prediction of the gut microbiota in Ovis ammon polii exhibit distinct seasonal variations. These findings provide a novel perspective for understanding how seasonal factors influence the health and nutrition metabolism of Ovis ammon polii and lay the foundation for health monitoring of Ovis ammon polii and the investigation of the specific physiological functions of its gut microbiota.