Objective To explore the phenotypic and genotypic characteristics in Chinese children with mitochondrial DNA depletion syndromes (MDS). Method The clinical and genetic data of all MDS patients diagnosed at department of Neurology of Beijing Children's Hospital, Capital Medical University from October 2010 to April 2018 were retrospectively collected and analyzed. Result Twelve patients with MDS were included in the study, including 8 boys and 4 girls. The developmental milestones were normal or mild retardation before disease onset. The age at onset was ranging from 0 to 2.9 years because of infection or without cause, and the most common initial symptom was failure to thrive, seizure, muscle weakness, psychomotor regression and hepatic dysfunction. At the last evaluation, all the patients had developmental retardation, failure to thrive, muscle weakness, dysphagia. Other clinical features were weight loss, hearing impairment, ptosis, seizure, breathing difficult, visual impairment, thick hair, lactic acidosis, hepatic dysfunction, high creatine kinase, high cerebrospinal fluid protein, abnormal metabolism and brain MRI, abnormal electromyogram. Five patients had death because of infection or multiple organ failure. Three families had SUCLG1 mutations. Two families had SUCLA2 mutations. One family had RRM2B mutations. Three families had POLG mutations. Two families had TWNK mutations. One familiy had TK2 mutations. 18 novel mutations were found. Conclusion We report 18 novel mutations in six different MDS related genes which expand the clinical and genetic spectrum of Chinese children MDS.