The human intestinal flora is a highly diverse ecosystem composed of trillions of bacteria. The imbalance of the flora is related to a variety of diseases. The intestinal flora interacts with the nervous system bidirectionally in many ways through the gut-brain axis. It causes neuroimmune inflammatory response, dysfunction of gut mucosa and blood-brain barrier, direct stimulation of the vagus nerve, spinal nerve of the enteric nervous system, and the neuroendocrine hypothalamus-pituitary-adrenal axis, causing neurological disorders. The metabolites of the intestinal microbial community also play a role. This article summarizes the characteristics of the altered intestinal flora and intervention measures in autism spectrum disorder, multiple sclerosis, Parkinson’s disease, epilepsy, Guillain-Barré syndrome, Alzheimer’s disease, neuromyelitis optica, hepatic encephalopathy, amyotrophic lateral sclerosis, schizophrenia, depression, chronic fatigue syndrome, Huntington’s disease and stroke. The current research on intestinal flora is still in its infancy, and very few studies were carried out on causality and the underlying mechanisms, which prevents the development of precise flora-based clinical intervention measures. It is expected the research on intestinal flora would lead to novel approaches for treatment of some neurological disorders.