Background <p>Seasonal behavioral divergence in zokors, driven primarily by their reproductive cycle, results in distinct ecological strategies between breeding and non-breeding periods. To elucidate how intestinal microbes adapt to these behavioral shifts, we used metagenomics to characterize the seasonal variations in the intestinal microbes of <i>Eospalax rothschildi</i>, a subterranean zokor endemic to China.</p> Results <p>Metagenomics revealed that summer samples showed an increased proportion of carbohydrate-degrading bacteria. Moreover, a significant difference in taxonomic composition was observed between the samples collected in the two seasons. Functional analysis based on the KEGG and CAZy databases revealed stronger carbohydrate degradation capacities in summer samples, notably through enhanced galactose metabolism capabilities. The enhanced galactose metabolism capabilities observed in summer were predominantly driven by increased abundance of α-galactosidase and β-galactosidase genes from enriched microbial populations, particularly <i>Bacteroides</i>, <i>unclassified_f_Lachnospiraceae</i>, <i>Roseburia</i>, and <i>Faecalibacterium</i>. Furthermore, iCAMP analysis revealed that deterministic and stochastic processes jointly governed intestinal microbial assembly in <i>E. rothschildi</i> during summer, as elevated nutritional demands potentially intensified host selection in the breeding season. Conversely, stochastic dominance in autumn may align with relaxed host selection.</p> Conclusions <p>Collectively, these results demonstrated that season played a crucial role in modulating the composition, function, and assembly process of the intestinal microbes of <i>E. rothschildi</i>.</p>