Modulation measurement profilometry (MMP), which encode the height information into the modulation information of sinusoidal grating on the measuring surface, is a vertical measurement technique. It is suitbed for measuring those objects with discontinuous height steps and/or spatially isolated surfaces. The application of MMP based on Fourier-transform is discussed in measuring complex surface, with presenting the concept of the depth-of-modulation and anlyzing its influence on measurement. Based on the depth-of-modulation, the detailed method and projects of designing measurement system are proposed to improve accuracy of measurement, and several practical questions influencing accuracy and solutions are discussed. The measured results show that the MMP based on Fourier transform measuring surface of complex objects can improve the accuracy of measurement greatly.