The diversity and composition of gut microbiota in hibernating mammals are affected by seasonal changes and fasting during hibernation. In order to examine the seasonal changes of the cecal microbiota of Daurian ground squirrel (Spermophilus dauricus), we analyzed the diversity, composition, and function of cecal microbiota from six groups of fattening stage (Initial fattening, Rapid fattening, Finished fattening) and hibernation stage (Early hibernation, Late hibernation, Arousal) using 16S rRNA gene high-throughput sequencing technology. In addition, the relationship between physiological characteristics and the composition and function of cecal microbiota was explored by redundancy analysis (RDA). The cecal microbiota was mainly composed of Firmicutes, Bacteroidetes, and Verrucomicrobia. Compared with other periods, the relative abundance of Firmicutes decreased and that of Bacteroidetes and Verrucomicrobia increased in Early hibernation. The Chao1 and ACE indices in Initial fattening, Rapid fattening, and Early hibernation were significantly lower than those in the Arousal, and the Simpson index in Finish fattening was significantly lower than that in Rapid fattening (P < 0.05) calculated by alpha diversity. Significant seasonal clustering of the cecal microbiota was found through the principal coordinate analysis (PCoA) of the weighted and unweighted UniFrac distance matrix. The butanoate metabolism and other metabolic pathways were enriched in fattening stage, and nitrogen metabolism and other related pathways were concentrated in hibernation stage as shown by PICRUSt analysis. The physiological characteristics at different stages were significantly correlated with the composition and function of cecal microbiota. In conclusion, it is indicated that hibernation profoundly affects the diversity and relative abundance of cecal microbiota. The changes in the composition and function of cecal microbiota play an important role in regulating the physiological metabolism, which can help Daurian ground squirrel adapt to seasonal environmental changes.