Abstract: The existence of goafs in mining areas pose serious threats to the safety of surrounding buildings, which is likely to induce structural settlement, cracking, and collapse. Accurately simulating the structural deformation and stress changes caused by uneven settlement is the basis for conducting structural safety assessments of hydropower stations in goaf areas. Taking the Damao Hydropower Station in Leshan City, Sichuan Province as an example, we propose a new foundation deformation inversion method to simulate the impact of uneven settlement in the goaf on the structure of the hydropower station accordingly based on the historical elevation data of the hydropower station and the measured relative elevation on site, as taking account of the incomplete data of the goaf. A three-dimensional numerical analysis model incorporating the structure and foundation rock mass of the hydropower station was established. The structural deformation triggered by uneven settlement of the goaf was inverted through iterative calculation, and the results were compared and analyzed with the traditional support settlement method. The results show that this method can accurately reflect the deformation and stress changes of the structure, and can be used to evaluate the safety of hydropower station structures under large-scale surface subsidence. Compared with the support settlement method, this method can better reveal stress concentration phenomena and the collaborative deformation characteristics of underground structures and rock masses. The research results provide new technological approaches for safety assessment and reinforcement renovation of similar projects.