This paper deals with the method to calculate the rotor eddy current losses of permanent magnet high-speed machines considering the effects of time/space flux harmonics. The flux harmonics caused by the slot geometry in the stator is calculated from the time variation of the magnetic field distribution obtained by the magneto-static finite element analysis and double Fast Fourier Transform. And, using the analytical approach considering the multiple flux harmonics and the Poynting vector, the rotor losses is evaluated in each rotor composite. Using this method is simple and workable for any kind of stator slot shape for rotor loss analysis.