The groundwater system of the Hami basin can be divided into three subregions based on hydrogeological conditions and structural characteristics. The investigation illustrates the controlling factors of hydrochemical and formation evolutionary mechanism of the groundwater system in the Hami basin through analysis and comparative study of different distributing disciplinarian characteristics of three subregions from the hydrogeochemical perspective. The results show that the distribution of hydrochemical characteristics in the Hami basin has obvious zoning features. The hydrochemical type gradually evolves from HCO₃ type to SO₄ type and eventually to Cl type while the TDS increases gradually from fresh water into brackish water and salt water in the water flow direction. The main source of water ion is from the dissolution of silicate rock and evaporite salt,and the hydrochemical compositions of groundwater in the study area are mainly controlled by evaporation and influenced by rock weathering and seasonal changes. The groundwater salt goes through filtration, migration and aggregation in the groundwater system, while the filtration effects become relatively weakened and the evaporation concentration increases gradually along the water flow direction. The chemical spatial evolution of groundwater in Hami basin is mainly driven by the influence of natural factors while the main driving factors for the time evolution are climate change and human activities such as industrial and mineral irrigation.