Objective To investigate the incidence and influencing factors of congenital hypothyroidism (CH), so as to provide basis for the prevention and treatment of CH. Methods From January 2015 to December 2019, the newborns undergoing neonatal disease screening in local region were enrolled in this study, and the incidence rate and distribution of CH were analyzed. Univariate and multivariate Logistic regression analysis methods were used to analyze the related factors of CH. Results The total number of neonatal screening from 2015 to 2019 was 127 524, of whom 45 cases were diagnosed with CH, and the overall incidence rates of CH in 5 years was 35.29/10⁵. The incidence rate of CH in winter and spring were higher than that in summer and autumn, but the difference was not statistically significant (χ²=0.884, P=0.347). The incidence rates of CH in preterm infants was the highest (251.68/10⁵), significantly higher than that of full-term infants(20.93/10⁵,χ²=105.839, P＜0.001).Multivariate Logistic regression analysis showed that low birth weight(OR=3.172, 95%CI: 2.185-8.116, P=0.012), premature delivery(OR=2.662, 95%CI: 1.904-7.115, P=0.008), gestational diabetes mellitus(OR=1.973, 95%CI:1.362-4.950, P=0.037), pregnancy induced hypertension(OR=1.892, 95%CI: 1.207-4.216, P=0.024),medication history(OR=2.350, 95%CI: 1.802-6.713, P=0.016), radiation exposure history(OR=2.712, 95%CI:1.938-7.346, P=0.028) and iodine deficiency during pregnancy(OR=4.120, 95%CI: 2.713-9.150, P＜0.001) were the risk factors of CH (P<0.05). Conclusions The incidence rate of CH is high in local region, and there are many risk factors that affect the incidence rates of CH. So it is supposed to make preventive measures based on these factors to reduce the incidence of CH.