Model generalization is simple in existing weir stability calculation methods, which cannot accurately reflect the flow field and stress distribution of an irregular barrage. Aiming at the problem, a gas-liquid two-phase flow was introduced to solve the surface flow field and the water pressure of the barrage based on finite element method and ANSYS Workbench software. The calculated results of the flow field were coupled into structural mechanics analysis to complete the stress and deformation analysis of an irregular barrage dam. The results show that the compressive stress can meet the foundation bearing capacity requirements under design flood level and ordinary water level working conditions, and there is no tensile stress inside the barrage dam. The overall deformation distribution of the barrage is reasonable, which can well reflect the discontinuity of the barrage body and the foundation. Therefore, this method can effectively solve the difficulty of stability analysis caused by the complex three-dimensional shape of the barrage and the uneven surface pressure distribution, providing the basis for barrage design.