There are large number of complex and diverse microbiota in gastrointestinal tract, and the gut microbes play an important role in maintaining gut environment homeostasis, not only affecting nutrient absorption and energy metabolism, but also regulating host physiological functions. Intestinal microorganisms can use nutrients of the host and then produce microbial metabolites, finally form host-microbe metabolic axis between host and gut microbes. The axis plays an important role in animal nutrition metabolism and immune homeostasis, and eventually affects the overall metabolism of host. We reviewed the concept of host-microbe metabolic axis, gut-liver axis, gut-brain axis, the interaction between gut microbiota and the host intestinal metabolism axis, and its impact on host health, with the aim to deepen our understanding about the contribution of intestinal microbes to host metabolism.