In each traditional timber structure in China, the mortise and tenon are one of the most important parts, because they connect differential components as a whole more big component. Of course, they made also beam and column as a frame. To conveniently utilize FEM for computing timber structure, mortise and tenon are considered as relative independent configurations, as well as the part which should be paid more attention. Because the connection between mortise and tenon is semi-rigid deformation behavior, rather than full rigid or ideally pinned connection, it is a key to accurately approach property of semi-rigid stiffness of mortise and tenon during the numerical simulation, for expressing the property of whole actual wooden structure. This study summarizes the research of the development of semi-rigid element and establishes easy computing and analytic finite element model of mortise and tenon. In addition, parameters of the model have been obtained by comparing numerical result applied MSC FEM software and the consequence of crossing timber frame experiment, based on the response surface method and optimize interactive theory. The analysis and the result mentioned above could be applied on the study of other entire large-scale ancient wooden architecture.