Abstract: In order to analyze the distribution and origin of arsenic, fluorine and iodine in groundwater in Datong Basin, groundwater quality zoning was classified. According to the latest series of test data of groundwater pollution, and the previous research of hydrogeology and hydrogeochemistry, the distribution of water chemical characteristic were compiled, including the contents of arsenic, fluorine and iodine in groundwater of Datong Basin, to reflect the spatial distribution regularity of high arsenic, fluorine and iodine contents groundwater in Datong Basin directly. The reasons for the formation of the high arsenic water were discussed through analyzing the relationships between pH, sulphate, nitrate, iron, manganese contents and arsenic contents. According to the relationships between pH, calcium ion, bicarbonate ion and fluorine, the causes of excessive fluorine were analyzed, and the similarity of distribution and origin of iodine and fluorine area was pointed out. The study results show that the surrounding strata with high arsenic and fluorine contents are the primary sources of arsenic and fluorine in groundwater. The specific lacustrine sedimentary environment provides the primary geological conditions for the enrichment of arsenic and iodine. The increase of fluorine in the northern part of Datong Basin is related to the moving of fluoride ion from the cohesive soil to the aquifer, because of the drop of underground water level. The high fluoride contents in the central region is related to the soil salinization. The lacustrine strata in the central region with rich salty clay is the primary geological factor of iodine enrichment, and the stagnant conditions of groundwater flow in alluvial depression area is the hydrodynamic factor of iodine enrichment. The intense evaporation and concentration under the dry climate conditions is con important factor for forming high fluorine and iodine contents groundwater. Based on the content distribution of the single component such as arsenic, fluorine, iodine, nitrate, nitrite, TDS, total hardness, ammonia nitrogen and so on, the authors carried out the quality division of the shallow and the middle and deep groundwater in Datong Basin by using the spatial analysis function of GIS. This paper would provide the geological basis for the development and utilization of the local groundwater.