Global warming and regional extreme climates will lead to unbalanced rainfall, melting glaciers, and permafrost degradation in alpine and arid mountain plains, thereby changing the regional hydrological cycle. The relationship between surface water and groundwater conversion is one of the important scientific issues of hydrological cycle climate response in alpine arid areas. Taking the Datong River Basin at the southern foot of the Qilian Mountains as the study area, based on 119 sets of basic hydrochemical parameters and deuterium-oxygen isotope data, using multivariate statistical analysis and isotopic techniques, the hydrochemical characteristics of surface water and groundwater in the basin and their mutual transformation process were studied. The results showed that the surface water was HCO3-Mg·Ca type, which was mainly controlled by rock weathering, whereas the groundwater was HCO3-Mg·Ca type and Cl·SO4-Na type, which was controlled by rock weathering and evaporation concentration. There was a small amount of calcium and magnesium feldspar dissolved in the upstream groundwater, and the chemical components of the midstream groundwater were mainly the weathering and dissolution of carbonate rocks. The contribution rates of weathering filtration, anthropogenic activities, native sedimentary environment, alternating adsorption of cations, and other factors to the chemical components of surface water and groundwater in the study area were 39.1%, 15.0%, 12.6%, 13.8%, and 19.5%, respectively. The deuterium and oxygen isotope contents of Datong River water showed a trend of enrichment to depletion along the groundwater flow direction. The δD and δ18O isotope test results showed that the deuterium and oxygen isotope content in the Datong River along the groundwater flow showed a trend of enrichment to depletion. The upper and middle reaches of the Datong River were mainly recharged by atmospheric precipitation, whereas the lower reaches were affected by geological structure and influenced by hydrogeological conditions, which was mainly due to diving and spring water overflow to supply river water, as the discharge area of groundwater.