The aims of this study were to describe the brain magnetic resonance imaging (MRI) features of methylmalonic aciduria and homocystinuria and to evaluate the additional value of H-MRS.Twenty-eight children with methylmalonic aciduria and homocystinuria were included in this study. The control group included 21 healthy children. All the cases underwent MRI and H-MRS before treatment. We measured the N-acetylaspartate (NAA), choline (Cho), creatine (Cr), and myoinositol (mI) peaks in the basal ganglia regions. The NAA/Cr, Cho/Cr, mI/Cr, and NAA/Cho ratios were calculated. We also observed whether there were lactic acid peaks.We identified that NAA/Cr and NAA/Cho significantly decreased in the basal ganglia and that 3 patients showed lactate peaks, but other metabolites were not significantly altered. Hydrocephalus and diffuse supratentorial white matter edema were the primary MR findings; 7 patients had thinning of the corpus callosum, and 2 patients had subdural hematoma. Six patients showed normal brain MRI findings.Methylmalonic aciduria and homocystinuria patients with metabolite changes in the basal ganglia demonstrate compromised neuronal integrity, and anerobic metabolism occurs in acute encephalopathic episodes. H-MRS is a useful tool for evaluating brain damage. Hydrocephalus and diffuse supratentorial white matter edema are the main MRI features.