Abstract: In order to characterize the structure of a Mo/Si multilayer, the Small Angle X-ray Diffraction(SAXD) of a multilayer sample is measured and the analytical methods of SAXD data were introduced, including Bragg peak fitting, Fourier transform, and X-ray diffraction fitting. The period thickness of the multilayer obtained by the Bragg peak fitting or X-ray diffraction curve fitting is 7.09 nm. The interface roughness(interdiffusion length) are 0.40-0.41 nm(Si on Mo) and 0.52-0.70 nm(Mo on Si), respectively. And the former is smaller than latter, which is consistent with the Transmisson Electron Microscopy(TEM) results in 0.40 nm(Si on Mo) and 0.6-0.65 nm(Mo on Si). Meanwhile, the refractive profile extracted by the X-ray diffraction fitting with a diffusion model is also consistent with the gray-scale profile by integrated High Resolution TEM(HRTEM). By the comprehensive characterization of the X-ray diffractometry(XRD) and TEM, the fine structural information of the Mo/Si multilayer is obtained, which is critical for the technology optimization of the multilayer deposition.