Objective: To assess the performance of non-invasive prenatal testing (NIPT) in screening sex chromosome aneuploidy (SCA), and explore prenatal decision-making in NIPT positive cases. Methods: The study retrospectively analyses singleton pregnancies who underwent NIPT screening. Clinical data, diagnostic results, and pregnancy outcomes were also collected. Results: There were 140 positive screens for SCA, including 62 cases of 45,X, 29 cases with 47,XXX, 28 cases of 47,XXY, 20 cases of 47,XYY, and one case of lower X chromosome. Karyotypic information was available in 103 cases. The positive predictive value was 26.09% for 45,X, 85.00% for 47,XXX, 85.00% for 47,XXY, and 68.75% for 47,XYY. The termination rates of 45,X, 47,XXX, 47,XXY, 47,XYY were 83.33%, 26.67%, 82.35%, and 54.54%, respectively (not including mosaic cases). Conclusion: Our findings demonstrated that the NIPT performed better in predicting sex chromosome trisomies than monosomy X even though false-positive cases do exist in NIPT. For prenatal decisions, pregnancies with diagnoses of fetal 45,X and 47,XXY were terminated more often than those with 47,XXX, 47,XYY. To better guide positive screening pregnancies, pre- and post-test counseling are essential in telling patients the benefits and limitations of the test, comforting their anxiety and giving them the choice for further diagnosis and pregnancy decision.