Flood discharge atomization is actually a process of mixed motion of water and air two-phase fluids. Based on the mass and momentum conservation equations, the mathematical model of flood discharge atomization was established and solved by the finite element method. A non-linear solution strategy was adopted, which solved the problems of numerical convergence and stability in the solution process. The correctness of the model was verified by comparing the result with that of the square cavity driven flow case. According to the spillways of the Shuibuya Hydropower Station and the topography of the valley, a three-dimensional finite element calculation grid was established, and the flood discharge process was simulated. The consistency of the calculated data with the actual flood discharge data verifies that the numerical method has good prediction ability for the wind and rain fields in the process of flood discharge atomization.