In order to study the water source identification in goaf of coal seam, taking Bayangaole coal mine as an example. Firstly, the water filling factors in the study area were analyzed, and the development height of the water-conducting fracture zone was determined through three methods. It was preliminarily judged that the Jurassic Yan'an Formation and Zhiluo Formation aquifers were the direct water-filled aquifers in the goaf. Secondly, based on the data of aquifer and goaf water samples in the study area, the hydrochemical characteristics and hydrogen and oxygen isotope characteristics of water samples were analyzed in detail. The results show that the high mineralization, weak alkalinity, sodium sulfate type water, and the composition characteristics of hydrogen and oxygen isotopes of the goaf water in the research area are similar to those of the Jurassic aquifer water, and there are significant differences from the Quaternary and Cretaceous Zhidan Group. Finally, based on the above analysis, it can be confirmed that the water source of goaf water in Bayangaole coal mine was mainly the Jurassic Yan'an Formation and Zhiluo Formation aquifers. The research results can provide a basis for the decision-making of water disaster prevention and control in similar coal mine goafs.