In Fourier transform profilometry (FTP), when zero component extends to fundamental component, it will influence measuring range and measuring precision, even makes the correct three-dimensional surface impossible. π phase shifting technique is usually used to eliminate the zero component. But this needs adding phase shifting device in measurement system and capturing two fringe patterns with π phase difference each other. Now a novel method is proposed, in which a bi-color fringe pattern is projected onto the object and the deformed color fringe pattern is captured by color digital camera. Two separate fringe patterns with π phase difference are extracted and used to eliminate the zero component. The method not only can eliminate zero frequency overlapping fundamental component using only one fringe pattern, but also simplify the experimental setup because of no need of phase-shift device.