Objective To evaluate the clinical effect of non-invasive prenatal testing (NIPT) by analyzing the efficiency of fetal chromosomal aneuploidy screening in Beijing. Methods The clinical data of 133 899 pregnant women, who underwent NIPT in eight prenatal diagnosis institutions of Beijing from January 2019 to December 2020, were collected and retrospectively analyzed. The test indications, results and prenatal diagnosis results were recorded. The positive rate of all pregnant women was calculated according to the test indications; According to the test results, it can be divided into trisomy 21 syndrome, trisomy 18 syndrome, trisomy 13 syndrome, sex chromosome abnormality, and other chromosome abnormalities. The prenatal diagnosis rate, positive rate, positive predictive value (PPV), sensitivity and specificity were calculated. Results Among the NIPT screening indicators, the detection rate of elderly pregnant women was the highest, accounting for 34.0% (45 509/133 899), followed by voluntary requirements, accounting for 32.7% (43 860/133 899). There were 1647 cases with high risk of NIPT, the positive rate was 1.2% (1647/133 899), and the positive rate of NT thickening and ultrasound structure abnormal were the highest in pregnant women. One thousand three hundred and forty-eight cases received prenatal diagnosis. The highest prenatal diagnostic rate was trisomy 18 reached to 91.5% (130/142), the lowest was the rate of sex chromosome abnormality reached to 76.4% (488/639). The overall prenatal diagnostic rate was 81.8% (1348/1647). The positive rates of trisomy 21, trisomy 18, trisomy 13, sex chromosome abnormality and other chromosomes abnormality were 0.2% (318/133 899), 0.1% (142/133 899), 0.1% (77/133 899), 0.5%(639/133 899) and 0.4% (471/133 899), respectively. The positive predictive values were 71.1% (226/318), 38.0% (54/142), 18.2%(14/77), 31.3% (200/639) and 17.8% (84/471), respectively. The sensitivity of trisomy 21, trisomy 18 and trisomy 13 was 98.7%, 96.4% and 100.0%, and all the specificity of was 99.9%. Conclusions The NIPT had high sensitivity and specificity but also still had the limitations of false positive and false negative. Therefore, prenatal diagnosis should be carried out for NIPT high-risk pregnant women, and it is important to strengthen the genetic counseling before and after testing.