1. MS-AFP MoM was higher in the fetal hypospadias group compared to that in the control group (1.14 vs. 0.96, p = 0.005).2. The AUC of fetal hypospadias predicted by MS-AFP was 0.644 (95% CI: 0.550–0.737, p = 0.005).3. When cutoff value 0.945 MoM was used for fetal hypospadias screening by MS-AFP, the sensitivity, specificity, and Youden index were 73.9%, 48.4%, and 0.223, respectively.4. The AUC of fetal hypospadias predicted by MS-AFP and β-hCG was 0.700 (95% CI: 0.610–0.789, p < 0.001) with a sensitivity of 55.1% and a specificity of 85.5%. Here, AFP is linked to hypospadias.