In order to simulate the cutting performance of a spindle mounted in the machine tool, the finite element (FE) model of spindles is required to be coupled with machine tool. However, the unknown joint dynamics (e.g., bolts) between the spindle and machine tool column limit the accuracy of the model. In this paper, an FE model updating method is proposed based on the identification of joint dynamics in both translational and rotational degrees-of-freedom (DOF). The receptance coupling (RC) technique is enhanced to estimate frequency response functions (FRFs) corresponding to rotational DOFs. The joint stiffness is identified through the iteration process by minimizing the difference between the simulated FRF and the measured FRF of the assembly. The proposed method is verified with a machine-tool spindle system. The good agreement between simulation and experiment shows the effectiveness of the method.