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To explore the pregnancy outcomes of women who couldn't obtain effective results from noninvasive prenatal testing (NIPT) and examine the factors leading to test failure. From April 2017 to December 2019, 120,041 pregnant women enrolled for voluntary NIPT. The case group comprised of 274 (274/120,041) women who failed to obtain effective NIPT results, and the control group (n = 540) was from the same population who obtained effective NIPT results and matched by age at a 1:2 ratio. Abnormal pregnancy rates between the two groups were analyzed using Chi-square analysis. NIPT failure risk factors were analyzed using logistic regression analysis. Logistic regression analysis showed that increased maternal age (OR = 0.988; 95% CI = 0.982–0.994), increased pregnancy age (OR = 0.989; 95%CI = 0.988–0.991), and decreased cell-free fetal DNA concentration (OR = 1.050; 95%CI = 1.043–1.058) were independent risk factors for NIPT failure. Fifteen cases showed fetus loss in cases of NIPT failure. There was a significant difference in abnormal pregnancy rate between the NIPT success and failure groups (χ2 = 50.943, P The specific interventions, guidance, and precautions are needed for pregnant women who have no effective NIPT results.