A design method to optimize the dimensions of a hybrid composite flywheel rotor and a permanent magnet is presented. The flywheel rotor consists of multiple rims of advanced composite materials with a permanent magnetic rotor attached inside the flywheel. The pressure distribution at the inner surface from the centrifugal forces of the magnet is considered together with the centrifugal body forces in the flywheel rotor. The size of the magnet also maintains the required induced voltage. An analytical solution of the displacements and stresses for each ring has been obtained and expressed in terms of a symmetric stiffness matrix. Using the stiffness matrix, the continuity conditions between the rings and the pressure due to the magnet can be easily considered. An optimum design is thus performed maximizing the total stored energy (TSE) with the size of the magnet and the thickness of each composite ring as design variables. For that purpose, the sensitivities of TSE and the Tsai-Wu failure index with respect to the design variables are derived by using the global stiffness matrix and the relationship of the magnetic size and the induced voltage. As a result, the optimal design using the hybrid composite rims has significantly reduced the stresses in a rotor and attained about 2 times the total energy of cases of using each material alone. The present optimization approach can be used to develop an efficient flywheel rotor for various applications.