[Objective] We studied the influence of three factors (region, gender and season) on intestinal bacterial community structure and diversity of Gansu zokor distributed in Liupan Mountains. [Methods] The V3-V4 regions of 16S rRNA genes from 36 Gansu zokors' cecum were sequenced using Illumina high-throughput sequencing technology. The sequences were used for analysis of species diversity, abundance and community structure of the intestinal bacteria. [Results] The intestinal bacteria of Gansu zokor mainly consisted of three phyla, among which Firmicutes was the most predominant phylum, and the others of Bacteroidetes and Proteobacteria. At the genus level, the predominant genera were Oscillospira, Ruminococcus, Coprococcus and Desulfovibrio. By comparing samples obtained from different regions, we found intestinal bacterial community structure presented a high similarity among the three counties (Pengyang county, Longde county, and Jingyuan county), whereas it showed a low similarity between Haiyuan county with other counties. Meanwhile, we concluded different sexes had different impacts on intestinal bacterial community structure of Gansu zokor, whereas female zokors are highly variable on the community structure of gut bacteria than male zokors. In addition, season might be an important modulator of the intestinal bacteria. The results showed that intestinal bacterial diversity of Gansu zokor was significantly higher in autumn than in spring, the similarity of bacterial community structure in autumn was also higher than in spring. [Conclusion] Region and gender merely had significant effects on intestinal bacterial community structure of Gansu zokor, whereas seasons might have significant impacts on both community structure and diversity of cecal bacteria significantly.