Objective To explore the clinical features of mitochondrial encephalomyopathy (ME) in children in southern China. Methods The clinical data of children diagnosed with ME from January 2015 to August 2022 were retrospectively analyzed. Results Thirty-six children with ME (22 boys and 14 girls) were included, and the onset age was 6.8 (2.1-10.8) years old. The onset symptoms were stroke-like episodes (24 cases), exercise intolerance (7 cases), ptosis (3 cases) and mental retardation (2 cases). Neuromuscular symptoms during the course of the disease included seizures (17 cases), headache (11 cases), paralysis (11 cases), ataxia (10 cases), ptosis of the upper eyelid (7 cases), mental/motor retardation (7 cases), blurred vision (6 cases), disturbance of consciousness (3 cases), and psychobehavioral abnormality (2 cases). Other non-neuromuscular symptoms included fever (7 cases), vomiting (6 cases), slow weight gain (5 cases), abdominal pain (2 cases), urinary retention (1 case), intestinal obstruction (1 case), and respiratory failure after sedation (1 case). The clinical phenotypes included mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) (16 cases), Leigh syndrome (LS) (11 cases), myoclonus epilepsy with ragged-red fibers (MERRF) (3 cases), Kearns-Sayre syndrome (KSS) (2 cases), and unclassifiable types (4 cases). The blood lactic acid of resting phase was increased in 71.4% of the children, and cerebrospinal fluid lactic acid was increased in 95.2% of the children. There was statistically significant difference between blood lactic acid of resting phase and cerebrospinal fluid lactic acid (P<0.05). Abnormal brain MRI was found in 31 children, mostly involving the parietal lobe (15 cases), occipital lobe (14 cases), basal ganglia (13 cases), brainstem (10 cases) and thalamus (8 cases). Long segmental spinal cord abnormal signals were found in 2 cases of LS. Typical broken red fibers were seen by muscle biopsy in 2 children. Genetic examination found mtDNA variations in 81.8% of the children. Conclusions The onset age of ME in children is around the age of 6. Stroke like attack is the commonest onset symptom. MELAS is the commonest clinical phenotype. The levels of resting blood lactic acid and cerebral spinal fluid lactic acid may increase. Head MRI shows that ME often involves the parietal and occipital lobe, basal ganglia, brainstem and thalamus. The results of genetic examination are mainly mtDNA variations.