Bacterial interactions in the biological network affect the growth of Bifidobacterium. In the present study, five habitats were constructed by changing animals, their health statuses and their diets. In each of these habitats, different networks of Bifidobacterium were outlined through correlation analysis of the 50 most dominant microbes. Thirty-eight bacterial genera directly correlated with the growth of Bifidobacterium, including 23 genera with a positive correlation and 15 genera with a negative correlation. This study presented, to our knowledge, a new biological network of rodent gut Bifidobacterium under various representative habitats. This study shows an in vivo network of Bifidobacterium, thereby contributing to constructing an in vitro network of Bifidobacterium for further studies.