Objective　To analyze the clinical features and genetic change of mitochondrial DNA deletion syndrome (MDS) caused by deoxyguanosine kinase (DGUOK) gene mutation. Methods　The clinical data of a case diagnosed with MDS by next generation sequencing of a boy were retrospectively analyzed. Results　A 36-day-old boy presented with hypoglycemia, abdominal distension, abnormal liver function, low blood glucose and high lactic acid. Gene testing identified two novel compound heterozygous mutations c.169dupT and c.630dupG in DGUOK, both of which were frameshift mutations resulted in truncated protein. Each parent was a heterozygous mutation carrier. SWISS-MODE predicted the damage effect on the structure of DGUOK. After 16 days of hospitalization, the boy was discharged from hospital without any improvement and then died. Conclusion　The MDS caused by DGUOK gene mutation is very serious with poor prognosis. It is necessary to screen genes early when abnormal liver function, hypoglycemia, hyperlactacidemia and other symptoms occur in newborns and infants. Early diagnosis is helpful for genetic counseling and guidance for prenatal diagnosis of the next pregnancy.