The weak part of the stiffness of machine tool combined structure is the key to improve the stiffness of machine tool. To overcome the static deformation with difficulty acquisition, the paper chooses machine tool combined structure which can be equivalent to one-dimensional bar structure, and a weakness index (WI) is proposed to identify the weak part of the stiffness by means of the dynamic hammer test method. Based on the bar structure as a numerical example, the weak parts are modeled as EA reduction in stiffness while the mass is maintained at a constant value. Thorough finite element (FE) method simulations are performed to assess the robustness and limitations of the method in several scenarios with single and multiple weakness. On the crossbeam of gantry type machine tool, the sensors are used to collect vibration data, the structural modal parameters are obtained by singular value decomposition (SVD) technique, and the dynamic characteristics are systematically reconstructed by using modal state space method to obtain stiffness data at zero-frequency. Then, the weak part of the structural stiffness is identified by the weakness index. Finally, the comparison of FE simulations and experiment results are provided to illustrate the working of the method.