The microbiota-gut-brain axis has received increasing attention due to its possible biological basis in regulating mental illness. The gut microbiota is closely related to neuropsychiatric diseases such as depression. It can affect the development of depression through interaction with the “gut-brain axis”. However, the mechanism between gut microbiota and depression is not yet very clear. In-depth studies of the realtionship between microbiota-gut-brain axis and depression help us to recognize and understand the depression from another perspective. Regulating the composition of gut microbiota to treat and prevent neuropsychiatric diseases such as depression is one of the future research directions, which also provides new ideas for exploring the mechanism of Chinese medicine treatment and prevention of depression.