The mammalian microbial communities in the gastrointestinal tract (GIT) play important roles in host nutrition and health. However, we still lack an understanding of how these communities are organized across GIT in natural environments. Here, using 16S rRNA gene sequencing, we analyzed the bacterial community diversity, network interactions and ecosystem stability across five gut regions (mouth, stomach, small intestine, cecum and colon) emanating from two common pika species in China, including Plateau pikas (Ochotona curzoniae) inhabiting high-altitude regions, as well as Daurian pikas (O. daurica) occupying low-altitude areas. The relative abundances of dominant Bacteroidetes and Firmicutes exhibited an increasing trend from mouth to colon. Cecum and colon harbored higher bacterial diversity compared with other anatomical regions. Gut region significantly influenced the structure of bacterial communities in the GIT. Network analysis indicated that topological features showed marked variations among gut regions. Interestingly, the ecosystem stability of bacterial communities increased gradually from mouth to colon. Our results suggest that gut region influences the diversity, structure and network interactions of bacterial communities in pikas. For hindgut-fermenting herbivorous mammals, relatively higher bacterial diversity and ecosystem stability in the cecum may provide a favorable condition for the fermentation of indigestible plant polysaccharides.