With the confidence enhancing on Chinse culture and the promotion of excellent traditional culture, the structural design and seismic performance of traditional multi-story pavilion-style timber pagoda persistently catch researchers’ attention. In this paper, a modeling method of pavilion-style timber pagoda was proposed, then verified by using the shaking tablet test results of a scaled seven-story Tang-style timber pagoda. Based on the verified modelling method, the influence of the changing of rocking and racking components on the seismic performance of traditional multi-story timber pagoda was investigated. It indicated that increasing the racking component could improve the structural stiffness and decrease the displacement response, but meanwhile obtained larger acceleration amplification coefficients and inter-story shear force; increasing the rocking component could lead to higher nonlinear response under high intensity earthquake, with the increasing of the excitation intensity, the acceleration amplification coefficients, inter-story drifts and shear forces of lower floors were increased. The research in this paper can be referred to the protection of multi-story historical timber structures and the structural design of new-built multi-story traditional timber structures.