A numerical method based on the assumption of a generalized plane strain (GPS) state is presented for calculating the stress and strength ratio distributions of the rotating composite flywheel rotor of varying material properties in the radial direction. The rotor is divided into many rings and each ring has constant material properties. All the rings are assumed to expand and have the same axial strain. A three-dimensional finite element method is then used to verify the accuracy of the present method. This method gives a better solution for most of the rotors than other methods of a plane stress or plane strain state. After verification, the effects of material properties on the total stored energy (TSE) of the composite flywheel rotor are investigated. For this purpose, the material properties of the rotor, i.e. circumferential and radial Young's moduli, ply angles and mass densities are expressed by power functions of the radius, and the rotor is analyzed. The analysis shows that TSE can be most effectively increased by changing the circumferential Young's moduli along the radius, which amounts to over 300% of TSE of the constant material properties. The variation of ply angles along the radius can increase TSE by about 30% at most. The method of changing the mass densities along the radius could be also effective but its effects are not so noticeable in the rotor where the circumferential stiffness is properly arranged.