Previous studies have indicated an association between iodine excess and increased incidence of thyroid dysfunction in adults. However, there have been few studies on how the intake of excessive iodine affects thyroid function in children. The objective of this study was to assess the effects of a long-term exposure to excessive iodine on thyroid dysfunction in children. Urinary iodine concentration (UIC) and thyroid function in 371 children from a high iodine (HI) area (water iodine: 150-963 μg/L) and 150 children from an adequate iodine (AI) area (water iodine: 12.8-50.9 μg/L) were measured. The water iodine concentration in the HI area was higher than that in the AI area (P < 0.001) and the median urinary iodine concentration of children in the HI area was 1030 μg/L, which was 8.6 times that of children in the AI area (123 μg/L) (P < 0.001). Children in the HI area had a higher concentration of sensitive thyroid stimulating hormone and higher positivity of both thyroid peroxidase antibody (TPOAb) and thyroglobulin antibody (TGAb). The prevalence of thyroid diseases was higher in HI area children than that in AI area children (P = 0.000), especially subclinical hypothyroidism (SCH; P = 0.004). A body mass index (BMI) of ≥ 22.3 kg/m(2) was associated with the incidence of SCH (OR: 5.51; 95% CI: 1.52, 19.9; P = 0.009). UIC ≥ 600 μg/L (OR: 3.62; 95% CI: 1.22, 10.8; P = 0.024) and TPOAb or TGAb-positivity (Ab+ OR: 6.48; 95% CI: 1.78, 23.6; P = 0.005) in children were significantly and independently associated with SCH. Interactions between UIC ≥ 800 μg/L and Ab+ (P-interaction = 0.004) were found. Furthermore, increased thyroid volume was correlated with higher UIC (β = 0.22; P = 0.002). Excessive iodine intake in children in HI areas is associated with impaired thyroid function; UIC ≥ 600 μg/L and Ab+ are the risk factors for SCH. Effective measures need to be taken for reducing excessive iodine intake.