In order to obtain a correct height distribution of a measured object using the conventional Fourier transform profilometry (FTP), the connecting line between the exit pupil of the projecting system and entrance pupil of the imaging device must parallel to the reference plane and in the same horizontal. Otherwise, severe error will be introduced. We propose a new height calculation method in Fourier transform profilometry for the case of nonparallel, deduce the expression of the reference fringe and deformed fringe, and then obtain the phase-height mapping formula. As a result, we find that the conventional Fourier transform profilometry method, in which the projector and CCD camera are at the same height, is a special example of our method. The new method improved the flexibility in Fourier transform profilometry. It is easier to obtain the full-field fringes through moving either the projector or the camera. Therefore the height distribution in the case that the projector and camera are not at the same height. Both computer simulations and experiments have proved our methods.