A phase difference correction method with the Flattop selfconvolution window is proposed in the article to solve the spectral leakage problem in FFT duo to the nonintegralperiod signal sampling. Firstly, the Flattop selfconvolution window is used to weight the sampled signal to suppress the spectrum leakage. Then, the formula for the calculation of frequency and phase of the signal are derived by the phase difference correction method. Finally, an approach by inverse derivation for the spectral amplitude correction with modified polynomials is set forth. A simulating example with Hanning window, Blackman window, BlackmanHarris window and Flattop selfconvolution window respectively is given and the results show that the method proposed in this paper is the best.