This paper indicates that the use of Euler angles lacks in its consistency and exactness of analysis when it was applied to incorporate the rotational equation of motion for rotor systems by previous researcher. Kinetic energy and angular velocity are different from case to case depending on the way of choosing Euler angles and thus only the linear system has been investigated even though the rotor system has a very nonlinear behavior. A new methodology is applied by using both spherical coordinate and quaternion in the rotor rotation to overcome weaknesses of Euler angles and shows its superiority It is found through numerical examples that the use of quaternion will be a more useful and valid tool to derive the numerical model of the rotor system.