Objective To analyze the efficiency and clinical value of noninvasive prenatal gene test (NIPT) in the diagnosis of fetal chromosomal aneuploidy. Methods From April 2016 to March 2018, 3 759 pregnant women who underwent noninvasive prenatal gene testing in our hospital were selected as subjects. The second generation sequencing AR550 platform combined with bioinformatics was used for noninvasive prenatal gene testing. The NIPT detection ranged from 21, 18, 13 to sex chromosome aneuploidy. For pregnant women at high risk of NIPT, amniotic fluid or umbilical cord blood puncture karyotype analysis was recommended to compare the consistency of the two results, and follow-up pregnancy outcomes. Results Among 3 759 pregnant women, NIPT showed 27 cases of high risk, with a positive rate of 0.71%. Twenty-four pregnant women were diagnosed as 21-trisomy in 14 cases, 18-trisomy in 1 case, 13-trisomy in 1 case and abnormal sex chromosome number in 4 cases. The positive predictive values were 100%, 50%, 100% and 66.7% respectively. Among them, 99 cases were non-invasive pregnant women with NT thickening, and 5 cases were at high risk of detection. The detection rate was 5.05% (5/99), which was higher than the overall detection rate. Conclusion NIPT has high sensitivity and specificity to 21-trisomy and 18-trisomy, can improve the efficiency of prenatal screening and diagnosis, and has good clinical application value.