An universal calculation formula and system calibration method are proposed, and the height-phase mapping relation in Fourier transform profilometry is derived. Because the request on the geometry structure of new universal calculation formula is not strict, the experimental setup is simple and the projector and the imaging device can be located arbitrarily to obtain better information of fringes. And this makes the operation flexible. The system parameters under universal condition can be obtained by the system calibration method. It can avoid measuring the system parameters directly, which makes the system easy to manipulate and improves the velocity of measurement. The new calculation formula and calibration method have been applied to measure the object with 28.00 mm height, and the relative error is only 0.97%. The experimental result proves that the new calculation formula and calibration method can exactly rebuild 3D shape of objects and the system has better universality.