Aiming at the influence of surface subsidence induced by open stoping with subsequent filling mining on surface industrial site in a phosphate mine, a three-dimensional model of top-down stoping with subsequent filling of ore body was established by FLAC3D. Numerical analysis was conducted on the deformation of overlying strata and surface subsidence in different mining stages, and the distribution laws of surface subsidence under different mining stages were obtained. As the advancement of mining, the cumulative goaf volume increases, and the maximum surface subsidence value gradually increases, showing a characteristic of larger subsidence values in the early and middle stages and smaller subsidence values in the later stage. The maximum surface subsidence value is 72.94 mm. Combining with the calculation results of displacement, inclination, and curvature near the industrial site on the surface, it can be concluded that the deformation values of the selected measuring points meet the protection level requirements of level Ⅰ and level Ⅱ, and the safety impact of designed underground mining scheme on the surface industrial site meets the regulatory requirements. The research results can provide useful references for the study of surface subsidence and ground pressure control during the top-down stage open stoping with subsequent filling process in similar large-scale mines.