Flywheel rotor structure is one of essential assemblies of the flywheel system used in IPACS. It is significant to ensure the safety of metallic hub and the composite rim under high centrifugal loading induced by the rotation field and the surface pressure produced by the interface misfits. In this paper a 3-D stress analysis model of the flywheel rotor is presented with the finite element analysis software ANSYS and the failure criteria of the materials are discussed to assess the structural strength. Moreover, the key design parameters are investigated briefly to disclose their influences on the stress distribution of rotor structure. At last, an optimum mathematics model with the outer radius of metallic hub, the thickness of each composite ring and the interface misfits as the design variables is presented. Based on the optimum design platform, the series of flywheel rotor structures can be designed systematically.