Objective To report the clinical features and the process of diagnosis and treatment of late onset methylmalonic aciduria complicated with methylenetetrahydrofolate reductase(MTHFR) deficiency in one case, which was suspected to be acute disseminated encephalomyelitis(ADEM). Methods The clinical and laboratory data of the patient was analyzed.Results The patient was a boy. When he was 12, he caught a cold, after which he had tiredness, poor spirit and memory, reduced school performance, weakness in lower limbs and memory, reduced school performance, weakness in lower limbs and difficulty in walking. One month later, he received an MRI of head and the whole spinal cord, which showed there was abnormal signal in cerebral cortex, posterior part of left paracele and T8-9 level spinal cord. Routine test of cerebrospinal fluid(CSF), biochemical and etiological test, and antibody detection related to immune encephalitis revealed nothing abnormal, and it was clinically diagnosed as ADEM, which was improved after treatment. When he was 13.5 years old, the symptoms aggravated without any cause. The body had difficulty in walking and felt weak in lower limbs. Reexamination by head MRI indicated slight encephalatrophy. The effect of intermittent treatment was not significant, and the muscular tension of lower limbs was increasing progressively. The detection results were as follows: urinary methylmalonic acid 29.63 mmol/mol creatinine (reference value 0.2-3.6 mmol/mol creatinine), 3-hydroxypropionic acid 6.68 mmol/mol creatinine (reference value 0.0-1.1 mmol/mol creatinine), serum free carnitine 16.17 μmol/L(reference value 20.0-60.0 μmol/L), propionyl carnitine 2.35 μmol/L(reference value 1.00-5.00 μmol/L); the level of serum homocysteine increased significantly(49 μmol/L)(reference value 0.0-15.0 μmol/L); there was heterozygous mutation of C.482G> A and c.626dupT in MMACHA gene, and heterozygous mutation of c. 665C > T in MTHFR gene. Finally, the boy was diagnosed with late-onset methylmalonic aciduria complicated with hyperhomocysteinemia and MTHFR deficiency. He was treated by intramuscular injection of hydroxycobalamin and taking levocarnitine, betaine and folic acid orally, as well as rehabilitation treatment, and got significantly improved after six months.Conclusion It is the first MMA case with the onset of ADEM, which is complicated with methylmalonic aciduria combined with two inheritary metabolic diseases: hyperhomocysteinemia and MTHFR. Metabolic screening is really necessary for the neuvous system diseases with atypical clinical symptoms.