In this study, the back electromotive force (EMF) waveforms of a flux switching permanent magnet (FSPM) machine and variable flux memory permanent magnet (VFMPM) machine with same main dimension were researched. Firstly, the simulation result showed that the maximum amplitude of phase back EMF waveform of FSPM machine was 245% larger than that of the VFMPM machine, and this was verified by the experimental result (243%). Secondly, the phase back EMF harmonics of the FSPM machine and VFMPM machine were compared, including the enhance flux condition and weaken flux condition of VFMPM machine. At last, the mutual demagnetization effect, which led to the difference amplitudes of maximum back EMF waveform between FSPM machine and VFMPM machine was analyzed. The comparison and analysis of the back EMF waveform will provide some qualitative advice for the future application research of the FSPM machine and VFMPM machine, such as application selection, optimization control method and so on.