The effect of nonlinearity in CCD on Fourier transform profilometry(FTP) has been discussed;It is deduced that the first frequency must be separated from the high frequency in the same period and the adjacent "frequency island".And the effect of sampling on the overlapping spectrum caused by nonlinearity in CCD has been gained.The analytial results indicate that due to the effect of nonlinearity in CDD(the second and the third frequency are primary),the sampling condition must be satisfied and the sampling frequency must be increased to avoid overlapping spectrum and to ensure the precision of measurement.The experimental result verified the correctness of the theory analysis.