80 shallow groundwater samples were collected from Tacheng Basin and analyzed for their chemical composition, and the distribution and source of Fe and Mn in groundwater in Tacheng Basin were studied. Generally, the shallow groundwater in Tacheng Basin is significantly polluted by Fe and Mn. 25% and 5% of the groundwater samples show Fe and Mn exceeding the groundwater standard, respectively. The concentrations of iron and manganese in deep confined water do not exceed the standard. The concentrations of Fe and Mn are controlled by the original geological and sedimentary environment and the superstition of human activities. High concentrations of iron and manganese in groundwater are distributed in stripes or patches in the copper and molybdenum metallogenic belts in northern mountains, middle alluvial plains and southern hilly areas of Tacheng Basin. The spatial distribution characteristics of iron and manganese in the groundwater of the study area are basically the same. The heavy pollution points of iron and manganese are mainly distributed in Tacheng of Emin County and its surrounding areas. The distribution of iron and manganese in groundwater in the study area is closely related to soil and aquifer composition, human activities and some other factors. Redox and groundwater runoff conditions are the main factors affecting the migration and enrichment of iron and manganese in groundwater. Infiltration of polluted water from sewage ditches is an important factor affecting the content of iron and manganese in underground water of heavy pollution spots in Tacheng Basin.