Excessive iodine can lead to goiters. However, the relationship between the water iodine concentration (WIC) and goiter rate (GR) is unclear. This study aims to explore the factors that influence children’s GR in areas with high WIC and analyse the threshold value of the GR increase associated with the WIC. According to the monitoring of the areas with high WIC in China in 2018–2020, a total of 54,050 children in eight high water iodine provinces were chosen. Drinking water, urine and edible salt samples of children were collected. The thyroid volume (Tvol) was measured. A generalized additive model (GAM) was used to analyse the relationship between the WIC and GR in children. Among the 54,050 children in areas with high WIC, the overall GR was 3.34%, the median of water iodine concentration (MWIC) was 127.0 µg/L, the median of urinary iodine concentration (MUIC) was 318 µg/L, and the noniodized salt coverage rate (NISCR) was 63.51%. According to the GAM analysis results, water iodine and urinary iodine are factors that influence the Tvol and GR, while the NISCR affects only the GR. When the WIC was more than 420 µg/L or the urinary iodine concentration (UIC) was more than 800 µg/L, the GR increased rapidly. When the NISCR reached more than 85%, the GR was the lowest. Thus, in areas with high WIC, WIC more than 420µg/L may increase the risk of goiter, and the NISCR should be increased to over 85% to avoid goiters in children.