Objective To explore the clinical features of Leigh disease caused by the mutation of m. 3688 G>A in NADH dehydrogenase 1 (ND 1) gene. Methods The clinical data of a child with Leigh disease caused by the mutation of m. 3688 G>A in ND1 gene were analyzed retrospectively. Results A 1 -year- and 3 -month-old boy presented with apathy as the first symptom, accompanied by psychomotor development retardation. Head MRI showed multiple abnormal signal shadows in the bilateral basal ganglia, thalamus, cerebral peduncle and cerebral cortex, and the lesions were roughly symmetrically distributed. An unexplained mitochondrial base mutation of m. 3688 G>A was found in ND 1 by gene test. Combined with clinical features and literature review, the child was diagnosed with Leigh disease with a new genetic variant. Through literature review, it was found that the number of mtDNA variants was a key factor in determining the clinical phenotype. Conclusion Mitochondrial gene detection technology is an important means to diagnose mitochondrial diseases.