Objective To study the clinical features and MRI diagnosis of mitochondrial encephalomyopathies (ME). Methods A total of 18 cases of ME patients admitted to our hospital during February 2011 to March 2015 were enrolled in the study. The clinical features of ME patients were retrospectively analyzed by electroencephalogram (EEG), electromyography (EMG), blood biochemical detection and imaging observation. The MRI findings and diagnosis value were explored. Results Among 18 cases of ME patients, there were 16 cases with abnormal EEG detected, the disease was mild in 5 cases, moderate in 7 cases, and severe in 4 cases. EMG showed 15 cases of myogenic injury and (or) neurogenic injury. Blood biochemical detection showed 14 cases of abnormally high LA, some patients with abnormally increased expression of CPK and LDH. Muscle biopsy showed abnormally increased RRF and mitochondria or structural abnormalities in 12 cases. MRI imaging showed low signal on T1WI and high signal on T2WI in 16 cases. 16 cases of lesions were mainly located in cerebral cortex and deep gray matter, there was involvement of white matter and brainstem in only a minority of patients. 15 cases showed symptoms of brain atrophy. Conclusion The main clinical symptoms of ME include epilepsy, mental disorder and limb movement restriction. In terms of routine clinical detection means, EEG shows abnormalities, EMG shows myogenic and (or) neurogenic injury, muscle biopsy shows increased RRF nuclear mitochondria or structural abnormalities, blood biochemical detection shows abnormally high LA, abnormally high expression of CPK and LDH in some patients. MRI images show certain signal intensity characteristics. It can well display the location of lesions and brain atrophy. In clinical practice, MRI images of ME can be combined with clinical features for effective diagnosis.