To improve the accuracy of seismic performance analysis of wooden structures, a multi-scale modeling analysis method was used in this paper. By using the multi-point constraint method, the mortise-tenon joints and beam-column members were set as the critical and non-critical regions, respectively. Based on the idea of multi-scale modeling, solid elements were adopted for fine-scale modeling in key areas, while beam elements were used for ordinary-scale modeling in non-critical areas. The coordination of macro-structure model and local micro-model could then be realized on different scales, and the seismic performances of solid elements and beam elements in modeling under different scales were compared. The experimental results showed that the multi-scale finite element numerical analysis can simulate the overall dynamic response of wooden structures and accurately analyze the boundary conditions. Through multi-scale and large-scale hierarchical modeling, local and global seismic performance analyses can be conducted, which are highly accurate and can improve the efficiency of seismic analysis.