We discussed the influence of the pixel size of CCD in the sampling process in Fourier transform profilometry(FTP) which is ignored in theoretic analysis earlier.And an integrated mathematical model of sampling of CCD is established to analyze the influence of the pixel size of CCD in FTP.Signal distortion and superposition of spectra are also discussed.Correlative expression and criterion of estimation are presented which presses FTP based on discrete Fourier transform closer to practice.