This study was performed to investigate the prevalence of congenital hypothyroidism (CH) in neonates in Nanjing, China and the long-term consequences of early treatment. A total of 442 454 neonates were screened for CH and 183 neonates were confirmed, with a prevalence of 1 in 2418. Of these, 163 neonates completed the follow-up process and 163 healthy children were recruited as the control group. The height, weight and body mass index (BMI) of the children with CH from 0.5 to 6 years were not significantly different from the control group (p > 0.05). The children with CH had a significantly increased risk for being overweight or obese between 0.5 and 6 years (p < 0.05). The children with CH showed a significantly lower developmental quotient (DQ) than the control group in all four areas of the Gesell test (p < 0.05). The results suggest that children with CH that has been identified by newborn screening and early treatment have normal growth and neuromotor development.