Objective: Early diagnosis and treatment of children with congenital hypothyroidism (CH) through newborn screening can effectively prevent delayed development. This study was designed to investigate the pathogenesis and factors that influence CH in urban areas of China between 2009 and 2018. Methods: A retrospective analysis of newborn screening data and diagnosis and treatment information for CH diagnosed in the information database of the neonatal disease screening center in one of China's five special economic zones from 2009 to 2018. Results: Of the 947,258 newborns screened between 2009 and 2018, 829 (406 girls) were diagnosed with CH at birth (1 diagnosis/1,136 births). Among the 608 cases of CH diagnosed at birth and re-evaluated at the age of 3 years, 487 were permanent congenital hypothyroidism (PCH, 1/1,429), and 121 were transient congenital hypothyroidism (TCH, 1/5,882). A total of 83.2% of infants with PCH (405/487) underwent thyroid imaging in the neonatal period, of which thyroid dysgenesis accounted for 28.64% (116/405) and functional defects accounted for 71.36% (289/405). The incidence of CH changed significantly in infants with initial serum thyroid-stimulating hormone concentrations of 41 to 100 mIU/L and ≥100 mIU/L, whereas the incidence of mild CH showed a slight increase. The incidence of CH was significantly higher in postterm infants (1/63) and low-birth-weight infants (1/370). Conclusion: In the past decade, the incidence of CH has increased, mainly due to the increase in the incidence of PCH and TCH. The incidence of mild CH has increased slightly. Postterm birth and low birth weight are important factors affecting the incidence of CH. Abbreviations: CH = congenital hypothyroidism; FT4 = free thyroxine; L-T4 = levothyroxine sodium; PCH = permanent congenital hypothyroidism; TCH = transient congenital hypothyroidism; TSH = thyroid-stimulating hormone; TT4 = total thyroxine.