Fourier transform is used to analyze the grazing incidence X-ray reflectivity curve of nanometer multilayer structures. The influences of preparing and measuring conditions on measuring results of multilayer structure parameters are simulated and the applicability and accuracy of Fourier transform is verified. The results show that the Fourier transform is more intelligible and quicker than traditional curve fitting method. The Fourier transform can exactly determine complex multilayer structure parameters without any subjective layer-structure model, which is a powerful analysis method for characterization of multilayer structures.