Objective To evaluate the clinical value of mass spectrometry in detecting genetic metabolic diseases in fetal amniotic fluid.Methods The supernatant of fetal amniotic was collected by amniocentesis,from the pregnant women in order to eliminate fetal chromosomal abnormalities.The levels of metabolites in the amniotic fluid was detected by mass spectrometry.The DNA of fetal amniotic fluid cells with abnormal metabolites was extracted,and genetic metabolic disease was performed by high-throughput sequencing,and verified by Sanger sequencing.Results The Propionylcarnitine(C3)was 3.89 umol/L,C3/C2 was 0.53,Methylmalonic acid was 7.33 mmol/mol creatinine by tandem mass analysis and homocysteine was 21.8 umol/L by fluorescence immunoassay in fetal amniotic fluid.These results suggested that the fetus is Methylmalonic Acidemia cblC Type,who was affected by c.80A>G(p.Gln27Arg)and c.658_660delAAG(p.Lys220del)of MMACHC gene by High-throughput sequencing and Sanger sequencing.The pregnant woman was a heterozygous variant carrier of MMACHC gene c.658_660delAAG(p.Lys220del),and the spouse was a heterozygous variant carrier of MMACHC gene c.80A>G(p.Gln27Arg).Conclusion MS can be applied to screening the pregnant women amniotic fluid and no reproductive history of genetic metabolic diseases such as MMA,to prevent the birth of fetuses with genetic metabolic,neither increase the pain of pregnant women sampling,nor interfere with other testing procedures.