Adequate iodine status is crucial for children's health and normal development. However, there is a paucity of research on the iodine status of children from areas with high groundwater iodine content. To monitor the iodine status of children in Shandong, China (regions primarily characterized by high iodine concentrations in groundwater) and to describe the factors influencing children's iodine status. A cross-sectional study was conducted from 2013 to 2023 on 3,253 children aged 3-13 years. We collected drinking water, spot urine, and 24-hour urine samples from children to assess their iodine status (measuring drinking water iodine concentration (WIC), water iodine intake (WII), urine iodine concentration (UIC), 24-hour urine iodine excretion (24-h UIE), daily iodine intake (DII), etc.), and analyzed influencing factors. The median WIC for children was 183 (IQR: 70.2, 362) μg/L, and the median spot UIC was 428 (IQR: 194, 737) μg/L, surpassing the WHO cutoff (300 μg/L). Children at risk of iodine excess numbered 1750 (61.8%). Approximately 61% of iodine intake came from drinking water. Boys had significantly higher iodine intake than girls (P < 0.001). Children's age showed positive correlations with spot UIC, 24-h UIC, and 24-h UIE. There were no significant differences in 24-h UIC and 24-h UIE among children with different BMIs. The logistic regression model revealed that the risk of iodine excess was increased by boy gender, increment in age (OR = 1.05, 95% CI: 1.02, 1.08), and every 10 μg (OR = 1.04, 95% CI: 1.03, 1.04) or 50 μg (OR = 1.19, 95% CI: 1.16, 1.22) increment in WII. Children in areas with high groundwater iodine content are at a risk of iodine excess. As age increases, the risk of iodine excess in children rises, with boys at a higher risk than girls.