Objectives To investigate the diagnosis and prognosis of mitochondrial acetoacetyl-CoA thiolase deficiency (T2 deficiency). Methods The clinical data from three cases in one pedigree were retrospectively analyzed. The related literatures were reviewed. Results Case 1 and 2 were probands, male and monozygotic twins. They were hospitalized because of fever, vomiting, and shortness of breath. The blood gas analysis showed a severely metabolic acidosis. The urine gas chromatography mass spectrometry analysis showed significantly higher level of 3-hydroxybutyrate, 2-methyl-3-hydroxybutyrate, tiglyglycine-1 and 3-tiglyglycine-1, and slightly elevated dicarboxylic acid. The blood tandem mass spectrometry analysis showed significantly increase of C5:1, C5-OH and C4-OH. Case 3 was the older sister of the twins, and was hospitalized because of severely metabolic acidosis at 5 months old. The ACAT1 gene analysis of 3 cases revealed the compound heterozygosity of c.622 C > T (p R208X) and c.653 C > T(p S218F). Conclusions T2 deficiency should be considered in children with an outstanding manifestation of acidosis. Urine gas chromatography mass spectrometry analysis and blood tandem mass spectrometry analysis should be performed for early diagnosis and treatment.