Mine water that inrushes from coal-roof strata has always posed a substantial threat to mining activities every year. Therefore, an accurate prediction of the water-conducting fracture zone (WCFZ) height in the mining overburden strata is of great significance for the prevention and control of mine water accidents. The support vector regression (SVR) is proposed to predict the height of the WCFZ based on the mining depth, hard rock proportional coefficient, mining thickness and length of the working face. Simultaneously, the multi-population genetic algorithm (MPGA) is employed to search for the optimal SVR parameters. The MPGA-SVR model is trained and tested with a total of 69 collected data samples, and it is also applied to a field test. The accuracy and stability of the model were measured by the mean squared error and correlation coefficients. The obtained results show that the MPGA-SVR model achieves a higher accuracy and stability than the traditional empirical formula and genetic algorithm (GA)-SVR model. In terms of the process for optimizing the SVR parameters, the MPGA can find the optimal parameters more quickly and accurately, and it can effectively overcome the problem of premature and slow convergence of the genetic algorithm (GA). The proposed model improves the prediction accuracy and stability, which will help to avoid accidents caused by the inrush of water inrush in mining overburden strata and protect the ecological environment of the mining area.