In order to analyze the effect of coupling relationship between joint stiffness parameters on the dynamic performance of machine tool bolt joints surface, a response surface method which is based on the theory of response surface statistics was proposed to fit the natural frequency of generalized modal states and the dynamic stiffness of the joints. In this method, the natural frequency was taken as the critical index to describe the object dynamic characteristics, with which the mathematic relationship between dynamic characteristics and the stiffness parameters between the joints were analyzed. The response surface model of predicating the varying dynamic characteristics with the finite element models of single and two nodes was established by central composite experiment design and response surface method theory. The least square method with the response function and the experimental test value were taken as the optimization objective, the nonlinear programming and genetic algorithm were combined to realize the stiffness parameter identification of the joint part. The type of response surface function expression was selected to display the stiffness coupling relationship between multiple pairs of nodes, and the influence with the coupling of stiffness on the dynamics of components was revealed. In order to verify the feasibility of the method, one bolt assembly was taken as the research object. The central composite experiment was designed to determine the different combination values of the stiffness between the joints, and the natural frequencies related to the first 11 orders were acquired by conducting the modal analyses with the ANSYS software. Utilizing the acquired dynamic data, a second-order polynomial response surface model was established to describe the connections between the stiffness and the natural frequencies. The accuracy of the established model was validated after calculating the valuating indexes, the influence of the coupling of stiffness on the dynamic characteristics of the components was analyzed, and the effects of multiple rigidness coupling, uncoupling and single stiffness on the dynamic performance of structures were compared and analyzed. The results showed that the dynamic modeling simulation with multi-stiffness coupling is in good agreement with the modal frequency and mode of vibration measured in the test. The first 11 mean modal frequency error is only 1.6%, which proves the necessity of considering the coupling relation between equivalent stiffness.