Background: The prevalence of hypertensive disorder in pregnancy has been well-documented worldwide. In Chinese newborns, the risk of hypospadias in women with hypertension during pregnancy remains ambiguous. This study aimed to evaluate the relationship between hypertension in pregnancy and neonatal hypospadias based on a large sample of Chinese people. Methods: A retrospective cohort study was conducted at our hospital from 2015 to 2019. Mothers who delivered male infants with hypospadias or those without any malformations were enrolled. Factors such as hypertension, placenta previa, thyroid diseases, hepatitis B, obesity, multiple birth, amniotic fluid, gestational age, birth weight, and in vitro fertilization were collected to establish a regression analysis to assess risk factors for hypospadias. Results: In total, 41,490 mothers and 42,244 male infants were enrolled. The overall incidence of hypospadias was 0.23%. The occurrence rate of hypospadias in pregnancy-induced hypertension (PIH) group was higher than control group (0.944% vs. 0.186%, RR 5.08), whereas the occurrence rate in chronic hypertension group was 0%. Potential exposure factors were screened for hypospadias, and PIH, multiple birth, hyperthyroidism, preterm delivery, low birth weight, and small for gestational age (SGA) were found to have higher proportion of hypospadias in offspring. After adjustment for potential confounders in the multivariate regression analysis, PIH (OR: 2.437, 95% CI: 1.478–4.016, P<0.01), birth weight (OR: 0.852, 95% CI: 0.795–0.912, P<0.01), and SGA (OR: 3.282, 95% CI: 1.644–6.549, P<0.01) showed a significant relationship with hypospadias. Conclusion: Women with PIH had higher risks of hypospadias in offspring. Lower birth weight, SGA and hyperthyroidism were also statistically associated with hypospadias.