This paper investigates and evaluates the correlation between the rotor magnet configurations and the characteristics and performance of a high-speed micro-turbine generator. Four configurations designed and studied include ring, segmented, modular, and asymmetric magnet shapes. The rotor is often manufactured by pre-magnetized permanent magnets (PMs), in which the magnets would be damaged when being assembled into the sleeve due to compressive force and magnetic force in some manufacturing process. Therefore, post assembly magnetization is applied to magnetize the PMs after the rotor being assembled into the sleeve. The effectiveness of this technique for different rotor configurations is firstly investigated. Then, the harmonic spectrums of back EMF, air-gap flux density, and cogging torque are evaluated. The relation among cogging torque, the vibration, noise and mechanical stress in these magnet configurations are analyzed. Finally, the generator performance is evaluated and discussed in the different resistance load conditions. Finite element analysis (FEA) is used to evaluate and validate the analysis results.