Ying-Xian timber pagoda is the existing oldest and highest wooden pagoda in China. Because of strong earthquake action and material aging, Ying-Xian timber pagoda is severely damaged and needs to be strengthened urgently. Aiming at the characteristics of complicated structural conformation and numerous damaged types of the pagoda, this paper discussed practical expression technology of computer simulation, determined the conformation character of layers-superposition and the modeling method of the pagoda based on the construction rule of traditional Chinese timber structures, and proposed the adjustment method to sectional area or elastic modulus of members according to the damage degree and position by the recognition research on damaged condition and stiffness variation of the pagoda. The finite element model of Ying-Xian timber pagoda was constructed and the dynamic behavior was analyzed by program ANSYS. The analysis results indicate that this FEA model is effective to describe the conformation character and damaged condition of the pagoda, and can be applied to seismic behavior study and security evaluation for the strengthening project of the pagoda.