In modulation measurement profilometry (MMP), the shape of a testing object is directly decoded from the fringe modulation instead of phase value calculated by fringes recorded from the surface of a diffuse object. A calibration procedure of the measurement system is presented based on MMP. Several parallel planes are used to establish the height-mapping between the measured height and the true height of the object. A look-up table of the height-mapping coefficient is established and stored in the measurement system. The measuring results show that the system error is compensated for and one order higher accuracy can be achieved by the presented system calibration method.