As we all know, the phase difference of two same frequency periodic signals equals to their initial-phase difference. For this reason, we give an initial-phase calculation method (IPCM) which is based on Harmonic Superposition Theory and the Newton Iteration Algorithm. The Non-integer Phase Difference Measurement (NI-PDM) method by initial-phase is as follows: (1) Synchronous sampling the waveform data of two periodic signals; (2) Getting high-precision amplitude and phase of each harmonic by using the non-integer harmonic analysis algorithm (NI-DFT); (3) Calculating initial-phase respectively by IPCM; (4) Calculating phase difference. Simulation results show that this method has a wide range of signal frequency drift and a high-precision, and can be used to measure the phase difference of waveform which meet the Diliheli conditions.