In order to explore the vertical variation of water evaporation losses in the river basin of the northern slope of Kunlun Mountains, the evaporation enrichment model and stable isotope (18O and 2H) methods were used to analyze the isotope data of different water bodies in the Cele River Basin from May to December, 2016. The temporal and spatial variation characteristics of isotopes in different water bodies was studied, the recharge sources of the basin was analyzed, and the evaporation losses of isotopes in different altitude areas were estimated using the evaporation enrichment model. The results showed that the isotope characteristics of different water bodies in the basin showed a pattern of dilution in the high mountainous area but enrichment in the desert area. There was a close hydraulic connection between the of Cele River water and groundwater; the average evaporation loss of the Cele River Basin at different altitudes was 24.99 % in the high mountainous area, 29.04 % in the middle mountainous area and 35.00% in the desert area. The results are of great significance for understanding regional water balance and its response to climate change in mountain ecosystems.