Based on the hydrogen and oxygen isotope data of water bodies, this study identifies the streamflow components of the mainstream channels using the MixSIAR mixed model for 22 sample sub-basins in the Tarim Basin. The relationships between streamflow components and basin characteristics for endorheic rivers were analyzed by further combining climate and underlying surface conditions of sub-basins. It appears that the sub-basins in the southern Tarim Basin primarily rely on precipitation for their streamflow, accounting for 39%−55%, 23%−30%, 22%−32% for precipitation, and glacial meltwater sources, respectively. The sub-basins located in the oasis area of the northern Tarim River are predominantly influenced by groundwater recharge, with a component proportion of 14%−32%, 44%−76%, 0%−39% for streamflow sources. Furthermore, the sub-basins primarily supplied by meltwater are predominantly found in the southwest region of the Tarim Basin, with a proportion of 29%−33%, 14%−31%, 40%−53%. Among various basin factors examined, actual evaporation, soil water content, vegetation index, and area proportion of desert area and glacier area emerged as key influencing factors on streamflow composition for the sub-basins of the Tarim Basin. It was also found that basin underlying surface conditions substantially impact variations in streamflow components. This result provides a scientific foundation for effective water resources management and ecological preservation within inland river basins amidst changing climatic conditions.