Abstract: Objective To explore the diagnosis and treatment of a rare case of methylmalonic aciduria combined with congenital adrenal hyperplasia. Methods The clinical and laboratory data of the first case of methylmalonyl CoA mutase deficient methylmalonic aciduria combined with 21-hydroxylase deficiency in China were analyzed. Results The male patient with age of onset at 3 months presented with feeding difficulty, diarrhea, metabolic acidosis, and psychomotor retardation after polio vaccination or high protein diet. At one year and 8 months of age, methylmalonic aciduria was diagnosed, and the patient was clinically improved after treatment. At 5 years of age, precocious puberty was noticed, and virilizing form of 21-Hydroxylase deficiency was diagnosed. Genetic testing confirmed 2 known mutations in MUT gene (c.866G > C, c.2179C > T) and 2 known mutations in CYP21A2 gene (c.188A > T, c.518T > A). Conclusions The clinical manifestations of inherited metabolic disorders and endocrine diseases are complex and it is rare that multiple disorders occurred simultaneously in one patient. This male patient has two rare diseases, methylmalonic aciduria and 21-hydroxylase deficiency.