The gut microbiota regulates intestinal homeostasis, and also participates in the modulation of brain function and behaviors of hosts. Disorders of gut microbiota are associated with the dysfunction of host nervous system, causing the development of neurodegenerative diseases. Thus, better understanding the role of gut microbiota in the gut-brain axis can provide new strategies for the diagnosis and treatment of nervous system diseases by the targeted modulation of gut microbiota composition and function. In recent years, studies on the interaction between gut microbiota and brain function have been reported, but the underlying mechanisms are still not fully understood. Therefore, combining with the latest research findings from our laboratory, we review here the modulatory effects of gut microbiota on nervous system and the potential role of interaction between gut microbiota and host in the modulation of brain function and behaviors of hosts, aiming to deepen our understanding about the role of gut microbiota in the modulation of brain function and behaviors in hosts.