Abstract: To address the limitations of traditional tetrahedral and hexahedral finite element meshes in terms of precision, geometric adaptability, and convergence speed, a polyhedral finite element program based on the Smooth Finite Element Method (S-FEM) was developed to enhance the efficiency and accuracy of seismic vulnerability analysis for concrete gravity dams. By integrating S-FEM with polyhedral elements, a high-precision polyhedral finite element model was constructed through implicit shape function construction and smoothing domain partitioning techniques. The convergence and computational efficiency of the program were validated using cantilever beam and complex geometric models. Furthermore, taking the Xichou gravity dam as a case study, the Incremental Dynamic Analysis (IDA) method was employed to evaluate the dam’s vulnerability under varying seismic intensities, with dam crest displacement and damage index as performance indicators. The results demonstrate that polyhedral elements exhibit significantly improved convergence speed compared to tetrahedral elements at identical mesh densities, along with insensitivity to mesh distortion. Under design seismic motion (0.14g PGA) and check seismic motion (0.16g PGA), the probabilities of minor damage for the case dam were 58.64% and 75.89%, respectively, while the probability of dam failure approached 0% in both scenarios. This study innovatively combines S-FEM with polyhedral elements, overcoming the geometric constraints of traditional mesh generation and significantly improving the numerical stability and computational efficiency for nonlinear analysis of complex structures. It provides reliable theoretical support and practical tools for seismic performance evaluation and design of high concrete dams, demonstrating substantial engineering applicability.