Objective: To investigate the positive predictive value (PPV) and clinical features of non-invasive prenatal testing (NIPT) as a screening method in detecting sex chromosome aneuploidy (SCA) within a high-risk population at the Maternity and Child Health Hospital of Anhui Province.Methods: From June 2015 to June 2019, 45773 women with singleton pregnancies volunteered to take an NIPT. Cell-free fetal DNA was extracted for high-throughput sequencing and amniocentesis karyotype analysis was performed in pregnant women. Results: 314 high-risk pregnant women underwent NIPT and 143 chose invasive prenatal diagnosis. Karyotype analysis was performed in amniotic fluid cells, wherein 7 cases of 45,X (PPV: 12.50%), 16 cases of 47,XXX (PPV: 55.17%), 25 cases of 47,XXY (PPV: 71.43%), and 10 cases of 47,XYY(PPV: 76.92%) were confirmed. The PPV of NIPT for SCA was 40.56%. The rate of SCA detected in women aged 40 years and older was 0.39%, which was significantly different from that detected in women aged <30, 30–34, and 35–39 years (P < 0.05). The detection rates of 47,XXX and 47,XXY were significantly correlated with maternal age (P < 0.05), but those of 45,X and 47,XYY showed no significant correlation with maternal age.Conclusion: NIPT can be applied for the detection of SCA, but the detection accuracy is low. Genetic counseling and further prenatal diagnosis should be provided.