This paper conducts a coupled vibration analysis of a two-stage bladed disk rotor system. According to the finite element method, the bladed disk rotor system is established. The substructure modal synthesis super-element method (SMSM) with a fixed interface and free interface is presented to obtain the vibration behaviors of the rotor system. Then, the free vibration results are compared with the ones calculated by the cyclic symmetry analysis method to validate the analysis in this paper. The results show that the modes of the two-stage bladed disk not only include the modes of the first- and second-stage bladed disk, but also the coupled modes of the two-stage bladed disk.