This study discusses the dynamic stiffness of the End-effector of a drilling robot for aircraft. In view of the requirements of automatic drilling processing for aircraft parts, based on the analysis of the working process of the automatic drilling End-effector, the End-effector of drilling unit has been employed in precision machine tools, It can provide very smooth motion and good verticality. In the design of the machines, it is necessary to obtain the stiffness of these guideway. Therefore, an identification method of the guideway stiffness is verified in this paper. In this method, the guideway stiffness is identified from the natural frequency of the moving body. First, a virtual prototype of the End-effector of drilling unit flexible is constructed by jointly using both ANSYS, which provides a foundation for further dynamic characteristic simulations. Next, the impact test is carried out for a drilling tool to obtain the vibration mode of its moving body, and simple vibration model is developed based on the obtained vibration mode to identify the natural frequency of the guideways. For further verification, natural frequencies of the moving body are calculated by FEM with the identified natural frequency and compared with the measured natural frequencies. The results shows that : the natural frequencies were calculated almost correctly with the identified equivalent stiffness, and which provides theoretical reference for improving the drilling efficiency and assembly quality of aircraft components.