We propose a universal calculation formula of Fourier transform profilometry and give a strict theoretical analysis about the phase-height mapping relation. As the request on the experimental setup of the universal calculation formula is unconfined, the projector and the camera can be located arbitrarily to get better fringe information, which makes the operation flexible. The phase-height calibration method under the universal condition is proposed, which can avoid measuring the system parameters directly. It makes the system easy to manipulate and improves the measurement velocity. A computer simulation and experiment are conducted to verify its validity. The calculation formula and calibration method have been applied to measure an object of 22.00 mm maximal height. The relative error of the measurement result is only 0.59%. The experimental results prove that the three-dimensional shape of tested objects can be reconstructed exactly by using the calculation formula and calibration method, and the system has better universality.