Abstract: Historical timber buildings are complicated and there are many types of existing damage, which bring challenges for Finite Element (FE) model to represent the actual mechanical condition and predict the structural damage accurately. For this purpose, an FE model updating method is proposed: the existing damage of historical timber buildings is obtained through 3D Laser scanning, and the FE model is updated through parameter optimization combined with Response Surface (RS) methodology and Multi-Objective Genetic Algorithm (MOGA). A structural damage prediction method of historical buildings is proposed based on the updated model. Using pavilion of Kaiyuan Temple in Quanzhou, Fujian as an example, the FE model was established and updated, and the damage development of pavilion was evaluated and predicted. The results showed that the discrepancies of pulled-out of mortise and tenon and inclination between the FE model and the actual structure were reduced by 79% and 69.5%, respectively, after model updating. The prediction indicated that the pulled-out of mortise and tenon and inclination will exceed the specification limits when the settlement of the pillar exceeds 2.5 mm.