The Tarim Basin in Xinjiang is located in the northwest inland arid region of China, but research shows that the region is rich in groundwater resources. To understand the hydrochemical characteristics and water quality of shallow groundwater in the desert area of the southern margin of the Tarim Basin, the groundwater was systematically sampled and tested. The ion characteristics and evolution mechanism of groundwater were analyzed by mathematical statistics, Schukarev classification, Piper three-line diagram, Gibbs model and ion ratio. Water quality was evaluated by the water quality index method (WQI) and irrigation water suitability-related parameters. The results indicated that the dominant cation in the study area is Na+, and the main dominant anions are SO42− and Cl−. According to total dissolved solids (TDS), the groundwater mainly belongs to brackish water and semi-saline water. The hydrochemical chemistry types are mainly Cl·SO4-Na·Mg type, followed by Cl-Na type, and the ion source is mainly the weathering and dissolution of evaporation rock, silicate and sulphate. The hydrochemical process is primarily controlled by evaporation concentration and rock weathering, and the cation exchange is weak. Furthermore, the WQI spatial distribution map shows that the groundwater in the middle of the study area is unsuitable for drinking and there are two areas with high WQI values greater than 500. In contrast, the good-excellent groundwater is scattered in the East. The groundwater generally has high to very high salinity, with significant changes in alkalinity. In addition, 54% of the water samples exceed the magnesium hazard (MH) limit. Therefore, certain measures should be taken before irrigation. This study has important implications for the rational development and reasonable utilization of local groundwater.