Mitochondria are responsible for cellular aerobic respiratory function. The nervous system is a huge energy consuming tissue of the body and highly depends on the structure and functional stability of mitochondria. Multiple research shows that mitochondrial abnormality is an essential reason for the occurrence and development of various neurological diseases. The mitochondria-targeted treatment for neurological disorders has become a frontier and hot spot. This review focuses on the research progress of mitochondrial transplantation in the treatment of various neurological diseases, mainly discussing its cellular and molecular mechanisms and the challenges which it faces, in order to provide clues and basis for clinical development of new therapeutic methods. There are 11 neurological models that have been reported to be effective for mitochondrial transplantation: middle cerebral artery occlusion cerebral ischemia reperfusion model, focal cerebral ischemia model, traumatic brain injury model, schizophrenia model, depression model, diabetic cognitive dysfunction model, Parkinson’s disease model, aging model, sepsis model, nerve compression model and spinal cord injury model. According to the source of transplanted mitochondria, the mitochondrial transplantation methods used in the above studies can be divided into direct transplantation and indirect transplantation. Direct transplantation refers to the transfer of mitochondria themselves, while indirect transplantation refers to the transfer of other carriers carrying mitochondria. There are three sources of mitochondria for direct transplantation: cell lines, human umbilical cord mesenchymal stem cells, and allografts. Mitochondria are derived from skeletal muscle, placenta, liver, brain and platelets. There are six methods of mitochondrial transplantation into the body: arterial injection, intraventricular injection, intravenous injection, vitreous injection, epineural injection, and spinal injection. The number of injections varies from a single injection to multiple injections in a row. The amount of mitochondria injected varied greatly. The duration of therapeutic or ameliorative effects after mitochondrial transplantation varied widely in reports. The effect after transplantation was to reduce the degree of disease in the animals. Biological mechanisms of mitochondrial transplantation consists of tunneling nanotubes (TNTs) and extracellular vesicles (EVs). And EVs are further classified into three categories according to their diameter size, including exosomes, microvesicles, and apoptotic body. The key issues to be addressed in mitochondrial transplantation for neurological diseases include: source of transplanted mitochondrial; pathway of mitochondrial transplantation; storage of the mitochondria; immune response. Mitochondrial transplantation has achieved great results in the treatment of neurological diseases in less than a decade, and it is considered to have great clinical value. This review predicts that future studies will gradually reveal mitochondrial quality control strategies and their molecular and cellular mechanisms in mitochondrial transplantation, and will form clinical standardized diagnosis and treatment plans for mitochondrial transplantation.