The effect of Pd2Si formation on the X-ray diffraction of Pd/Si periodic multilayer films after annealing has been studied by X-ray diffraction in small and high angle regimes. The results show that the influence of Pd2Si in small period multilayers is more severe than that in large period multilayers. The periods of multilayers have been calculated with one peak posi-tion or with two peak positions after introducing the refractive correction, and the latter is more accurate than the former. The results of simulation show that an uniform Pd2Si layer formation in a period is not enough to explain the large variation of intensity after annealing. Roughness of the interface is another important factor to influencing the diffraction intensity.