The China Geochemical Baseline project (2008–2013) obtained a large amount of reliable baseline data on 76 elements, including iodine, from 3381 top (0–25 cm) and 3380 deep (>100 cm) alluvial soil or sediment samples. Iodine concentrations, ranging from 0.01 to 21.58 mg/kg in the top samples (TS) and 0.01 to 28.30 mg/kg in the deep samples (DS), were determined using colorimetry under strict quality control. The median values of iodine, which were considered geochemical baseline values in the TS and DS, were 1.10 and 0.99 mg/kg, respectively, and the mean values were 1.45 and 1.43 mg/kg, respectively. The majority of the iodine in the pedosphere is obtained from the atmosphere, which in turn is obtained from the oceans. The mobility of iodine in different media was determined by its geochemical behavior. Iodine distribution maps indicated that low iodine concentrations below Q25 (<0.65 and 0.56 mg/kg in TS and DS, respectively) are primarily distributed in Northwest China, Tibet, and Sichuan, which could be mainly attributed to significant atmospheric washout and/or distance from the sea and low iodine fixing capacity of inland deserts. High concentrations are scattered throughout the country and are influenced by various factors, including atmospheric precipitation, soil composition, and mineral distribution, exploitation, and utilization. After the advent of salt iodization in 1995, iodine deficiency disorders have been largely eliminated from China. Although the heavily diseased areas correspond to some low iodine concentration areas, the distribution of the overall iodine deficiency disease areas from before salt iodization, compared using geochemical maps, is not correlated to the distribution of iodine concentration in the soil. These new TS and DS data and iodine geochemical maps provide a deep insight into the factors controlling the distribution of iodine in the pedosphere of China and significantly improve the global database of iodine in soils.