To investigate the stability mechanism of historic timber buildings, different numerical analysis models were built and analyzed firstly based on the 1:10 local interlayer structure model of Yingxian wooden pagoda, it is demonstrated that the finite element analysis with the discrete solid elements is more appropriate for load-bearing mechanism research on historic timber building by the inversion analysis and comparison of the test data with different models. Then, the multi-scale model of the whole structure of “discrete solid – continuous 2D members” of the wooden pagoda was established, and the whole process of “the loading and horizontal displacement of the structure” were calculated and analyzed respectively in the case of one model with no initial defect and the other one with initial defect of horizontal displacement between the structural layers. The results show that the static load, which is consist of wind load with a 50-year return period, may aggravate the present damage state of the historic timber building. Existence of initial defects will obviously reduce the stable bearing capacity and deformation capacity of the historic timber building.