Fourier transform profilometry (FTP) is a kind of active technology by projecting a grating on object surface to measure the three-dimensional (3D) shape. It requires only one structured fringe pattern to analyze the entire range of the measurement system. Based on the subtraction of the distortion grating phases of the object surface and the reference surface, FTP can measure the height distribution. But in divergent light path the coordinate of the height is only an approximation, so that in precise measurements we need theoretical correction. We analyzed the cause of the height measurement error introduced by the coordinate confusion, and made the first order correction. In experiment, we used bi-color fringe technology, in combination with the Matlab software, to and successfully carried out a quantitative analysis of the error.