Surface waterlogging disasters due to underground mining and geological status have caused the abandonment of fertile land, seriously damaged the ecological environment, and have influenced the sustainable development of coal resource-based cities, which has become a problem that some mining areas need to face. However, the traditional underwater terrain measurement method using sonar encompasses a time-consuming and labor-intensive process. Thus, an inversion method for obtaining the underwater spatial information of subsidence waterlogging in coal mining subsidence waterlogging areas is proposed, based on differential interferometric synthetic aperture radar (D-InSAR) and the probability integral prediction method. First, subsidence values are obtained in the marginal area of the subsidence basin using D-InSAR technology. Then, the subsidence prediction parameters of the probability integral method (PIM) are inverted by a genetic algorithm (GA) based on the subsidence values. Finally, the underwater spatial information of subsidence waterlogging is calculated on the basis of the prediction parameters. The subsidence waterlogging area in the Wugou coal mine was adopted as the study area, and the underwater spatial information of subsidence waterlogging was inverted by the proposed method. The results show that this method can effectively provide the underwater spatial information of subsidence waterlogging, including the maximum subsidence value, waterlogging volume, subsidence waterlogging area, and underwater terrain in the subsidence waterlogging area. Compared with field-measured data from the same period, the RMSE of water depth is 99 mm, and the relative error is 9.9%, which proves that this inversion method is accurate and can meet engineering precision requirements.