Iodine deficiency disorder (IDD) is a serious public health issue in China. As iodine in the environment is the fundamental cause of iodine-endemic diseases, investigating the distribution and controlling factors of iodine in the soil of endemic disease areas for the accurate prevention and control of endemic diseases is important. This paper aimed to examine the concentration and spatial distribution of iodine in soil of China, along with its correlation with IDD, and explore the influence of geological background, soil types, and geomorphoclimatic landscapes. Based on the data of China Geochemical Baseline (CGB) project, China can be divided into seven high- and three low-value zones. We found that the formation of low-value zones is associated with the high mobility of iodine. According to the Specification of Land Quality Geochemical Assessment, I-deficient soil accounts for nearly 70 % of the land area in China. Meanwhile, the distribution of severe endemic diseases was more consistent with that of iodine concentration (<0.654 mg/kg) in top samples. The high-value zones were closely related to biological affinity and adsorption of iodine, and were mainly distributed in areas with high organic carbon content and coastal areas. The distribution characteristics of iodine in soil and that of IDD were also linked to the geological background, soil types, and geomorphoclimatic landscapes. The predominant soil type in seriously endemic diseases areas was Argosols, and the predominant geomorphoclimatic landscapes was alpine canyons, accumulated Gobi desert, and karst regions. Apart from the karst terrain, other soil types and geomorphoclimatic landscapes mentioned above exhibited low-iodine concentrations.