To evaluate the application value of non-invasive prenatal testing (NIPT) in prenatal screening of pregnant women with high risk. Methods: The clinical data of 3985 pregnant women who performed NIPT due to critical risk or high risk assessed by prenatal screening during the second trimester of pregnancy from February 2015 to December 2019 were analyzed retrospectively. And these women were divided into 4 groups by the results of prenatal screening, which included group A (women with high risk of trisomy 21), group B (women with high risk of trisomy 18), group C (women with moderate risk of trisomy 21), and group D (women with moderate risk of trisomy 18). If the women with high risk of trisomy 21 or trisomy 18, amniotic fluid chromosome diagnosis would be performed further for assessing the detecting efficiency of NIPT for common fetal chromosome aneuploidy, such as trisomy 21, trisomy 18, trisomy 13, and sex chromosome abnormality (SCA). Results: The NIPT results of 3985 pregnant women indicated that the fetal chromosome aneuploidy rate was 1.38% (55/3985), among which, that of women in group B was 16.28% (7/43), that of women in group A was 2.58% (25/968), that of women in group D was 1.96% (1/51), and that of women in group C was 0.75% (22/2923), respectively. In the 55 pregnant women with high risk by NIPT, 46 cases were confirmed by karyotype analysis of amniotic fluid, which included 27 cases with chromosomal abnormalities, 16 cases with trisomy 21, 6 cases with trisomy 18, and 5 cases with chromosomal abnormalities. The positive predictive value of NIPT for diagnosing common chromosome aneuploidy was 58.70% (27/46), while the positive predictive value of NIPT for diagnosing trisomy 21, trisomy 18, and sex chromosome aneuploidy were 84.21%, 75%, and 33.33%, respectively. Conclusion: Compared with the traditional maternal serum biochemical method, NIPT technology has good detection efficiency for common chromosomal aneuploidy. In order to reduce their pressure and abortion risk due to invasive prenatal diagnosis, the screening common chromosomal aneuploidy by NIPT technology can be used for pregnant women with high or moderate risk by prenatal screening. However, NIPT technology detection and screening target diseases are limited, so it can only be used as an advanced screening program for common chromosomal aneuploidy presently, and cannot replace the prenatal diagnosis technology.