Effective phase compensation of the incomplete single and double frequency signal was investigated effectively. The necessary condition for exact phase compensation of signal was deduced and testified theoretically. That is, exact phase compensation can be executed for the incomplete single frequency unconditionally. And it can be executed for the incomplete double frequency on condition of that the multiply of difference from the two frequencies of the signal and sampling time interval is an integer. Because the exact phase compensation can’t be carried out, the approximate compensation method based on waveform evaluation criterion was proposed. By simulation, the different compensation effects based on four different criterions were compared. The results proved that the deduced theory and proposed method are valid, and the compensation effect based on waveform exponent entropy or energy contrast criterion is better than that of other, and the peak of frequency spectrogram is higher than that of other.