Objective: to discuss the value and significance of non-invasive prenatal testing (NIPT) in screening fetal sex chromosome diseases. Methods: a total of 19327 pregnant women who underwent NIPT in our hospital from February 2018 to January 2021 were selected. Pregnant women at high risk of NIPT suggestive chromosome abnormalities underwent amniocentesis after informed consent for fetal amniotic fluid chromosome karyotype analysis and chromosome microarray analysis (CMA). The test results and pregnancy outcomes of all cases were summarized and analyzed. Results: among the 19327 pregnant women, 92 pregnant women with high risk of sexual chromosome abnormalities suggested by NIPT, and the positive rate was 0.48%. Among them, 81 pregnant women underwent amniocentesis, karyotype analysis and CMA detection. 45, X 13 cases (including 2 chimeras), 47, XXX 5 cases, 47, XXY 8 cases, 47, XYY 6 cases, sex chromosome microdeletion and microduplication 6 cases and other chromosome abnormalities 6 cases were diagnosed. The total positive predictive value (PPV) of NIPT was 45.68%; The PPV of 45, X (including chimera), 47, XXX, 47, XXY, 47, XYY and sex chromosome microdeletion and microduplication were 30.95%, 50.00%, 80.00%, 75.00% and 54.55% respectively. The PPV of NIPT for sex chromosome aneuploidy (including chimera) and microdeletion microduplication were 44.29% and 54.55% respectively, and the difference was not statistically significant (P > 0.05); The PPV of chromosome number increase and chromosome number decrease (including chimera) were 67.86% and 30.95% respectively (P < 0.05). The proportion of sex chromosome abnormalities found by chromosome karyotype analysis and CMA detection were 38.27% and 44.44% respectively. Conclusion: NIPT has a high positive predictive value for sex chromosome diseases, but the positive predictive values for different types of sex chromosome abnormalities are quite different. NIPT can be used as a screening method before invasive prenatal diagnosis. Pregnant women with positive test should receive invasive prenatal diagnosis to further clarify the diagnosis. CMA has a higher abnormal detection rate than the traditional karyotype analysis. It is suggested to carry out two joint examinations for pregnant women with high risk of sexual chromosomes prompted by NIPT.