Surface water and groundwater are the main components of water resources. It is of great theoretical significance to study the mutual transformation process of surface water and groundwater in arid areas for the rational development, utilization, and evaluation of water resources. Based on surface water and groundwater in Ebinur Lake basin, the stable isotope composition characteristics, distribution law, and the recharge relations of different water types were discussed. Results showed that: (1) The δ²H and δ¹⁸O values of precipitation in the Ebinur Lake basin showed significant seasonal variation, presenting dilution in winter and enrichment in summer through the whole year.(2) In the Ebinur Lake basin, the stable isotopes values of lake were significantly higher than that of river, which reflects the strong water evaporation concentration of lake. In Bortala river and Jinghe river, the δ²H and δ¹⁸O from upstream to downstream tended to enrichment, but it showed different features among the areas of mountain, oasis and plains. The δ²H and δ¹⁸O of groundwater presented the minimum in mountainous part, the middle in plains, and the highest surrounding the Ebinur Lake. (3) In Bortala river, the exchange proportion of groundwater and river water in the upper reaches was large, which was 63.0%. The exchange ratios in the middle and lower reaches were relatively low, which were 5.0% to 33.0% and 2.5% to 26.0%, respectively. In Jinghe river, the deep groundwater was replenished by shallow groundwater and river water, the recharge ratios were 73.3% and 26.7%, respectively. In the vicinity of Ebinur Lake, the diving flow was cut off and exposed to spring water, which supplies the lake with the river water. The study revealed the exchange relationship between surface water and groundwater in Ebinur Lake basin, which can provide scientific support for water resource management and ecological environment construction of the Ebinur Lake basin.