The more complex the hydrogeological conditions of a mine, the more likely the coal seam is to experience water inrush during the mining process, and the greater the degree of the water inrush hazard. The scientific and reasonable prediction of water inrush in mines with complex hydrogeological conditions is of great significance to the safe and efficient operation of coal mines. Taking the roof water inrush problem of the No. 3 lower coal seam in the Jisan Coal Mine as the research object, the factors affecting the roof water inrush of the coal seam were comprehensively considered from three aspects: the aquifer property, the mining fracture development and the geological structure. The evaluation index system was constructed by selecting 10 factors, including the aquifer depth and thickness, core recovery rate, brittle–plastic rock thickness ratio, number of water-resisting layers, development height of the water-conducting fracture zone, fault density, frequency density, scale index and variation coefficient of the coal seam floor dip angle. At the same time, based on the dual influence of subjective and objective weighting, the scientific and reasonable weight of each factor was ensured. The AHP-CRITIC composite weighting method was used to calculate the comprehensive weight of each factor. Finally, the roof water inrush risk prediction model was constructed. According to the prediction results, the study area was divided into a low-risk area, medium-risk area and high-risk area. Compared with the actual situation, the prediction results were basically consistent with the actual situation, and the prediction results can provide the basis for the prevention and control of water in a coal mine.