The Ili Valley in northwestern China plays a vital role as a green oasis in the large-scale moisture cycle and water utilization in Central Asia's core. To clarify the distinctive hydrochemical characteristics and genesis that differentiate it from the neighboring arid areas, the first large-scale sampling of river water covering the entire Ili Valley was conducted. The results show that the hydrochemical and stable isotopic characteristics vary spatially and seasonally among the tributaries. Rock weathering mainly controls the major ion composition in river water, which gradually varies along the river due to evaporation and snowmelt. The S2H and S18O values range from -103.00%o to -72.00%o and -15.00%o to -9.60%o, respectively. Contrary to what is expected, the S2H & S18O in the Tekes & Ili Rivers are enriched with altitude, showing an "inverse altitude effect" influenced by topography and moisture sources; the Karsh River has lower S18O values due to snowmelt; the Kunes River has a U-shaped trend of isotopic concentrations and high d-excess values by precipitation. Both the seasonal deviations in river waterlines (RWL1 vs RWL2) and the backward trajectory by HYSPLIT 4.0 showed that the origin of spring moisture at low troposphere in the Ili Valley could be traced to the surrounding regions, the summer moisture mixed with frigid air from the Arctic Ocean, while sub-cloud evaporation and surface-groundwater interaction are also the factor internally within the basin. The findings complement the basin-scale hydrochemical monitoring data and help investigate the large-scale hydrological cycle.