Abstract: Gut microbiota is a complex community which plays an important role in the normal physiological functions of human beings. The normal gut microbiota has many important functions which involving host nutrient metabolism, drug metabolism, maintenance of structural integrity of the intestinal mucosal barrier, immunomodulation, protection against pathogens, etc. Gut microbiota exerts effects on the brain which not only through the nervous system, but also through the endocrine system, immune system and metabolic system. A bidirectional communication between the gut and the brain is referred to as the brain-gut axis. The brain-gut axis may be a key regulatory pathway between the brain and the gastrointestinal tract, while gut microbiota is an important participant in this pathway. The changes in gut microbiota can act on the central and peripheral nervous system through immunologic mechanism, which leading to changes in the brain function, and consequently participating in the pathogenesis of various central nervous system diseases, such as Parkinson's disease, Alzheimer's disease, schizophrenia, and multiple sclerosis, etc. Epilepsy is a chronic neurologic disease characterized by a persistent tendency to cause epileptic seizures. Immunologic mechanism plays an important role in the generation and development of epilepsy, especially autoimmune epilepsy. Autoimmune epilepsy is one of immune-mediated epileptic diseases characterized by repeated and continuous epileptic onset, its clinical features includes frequent onset of focal seizures, encephalopathy, progressive cognitive impairment, focal neurological injuries and/or other central neurologic deficits. The excessive activation of immune response(the innate and acquired immunity)participates in the pathogenesis of autoimmune epilepsy, the neural-specific antibodies can be detected in the cerebrospinal fluid of the patient with autoimmune epilepsy. Anti-inflammation or immune therapy may have a good clinical therapeutic effect in some drug resistance epilepsy, especially in diagnosed autoimmune epilepsy. Immune therapy and the reconstruction of intestinal microbiota may be a promising strategy for treatment of epilepsy in the future.