Early diagnosis and treatment of children with congenital hypothyroidism (CH) through newborn screening can effectively prevent delayed development in children. This study was designed to investigate the pathogenesis and influencing factors of CH in urban areas of China between 2009 and 2018. 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. Of the 947,258 newborns screened between 2009 and 2018, 829 (406 girls) were diagnosed with CH at birth(1/1136). Among the 608 cases of CH diagnosed at birth and reevaluated at the age of 3 years, 487 were perma(PCH, 1/1429) and 121 were transient (TCH, 1/5882).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 TSH concentrations of 41-100 mIU/L and ≥100 mIU/L, while the incidence of mild CH showed a slight increase. The incidence of CH was significantly higher in post-term infants (1/63) and low birth weight infants (1/370). 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. Post-term birth and low birth weight are important factors affecting the incidence of CH.