Thermal stability of Co/C multilayers prepared by a dual-facing-target sputtering system was studied. A picture of the thermally induced changes in the microstructure was obtained using complementary measurement techniques including low-angle and high-angle X ray diffraction, transmission electron microscopy, Raman spectroscopy and X-ray photoelectron spectroscopy. It was found that the period expansion, reflectivity change and compound formation that were observed after annealing are caused by structural changes both in the sublayers and at the interfaces. Below 400℃, the period expansion is mainly caused by the graphitization of the amorphous carbon layers, and a significant increase in the reflectivity at grazing incidence was observed. By 500℃, the crystallization and agglomeration of Co layers induce an enormous period expansion and a serious decrease in reflectivity. A small amount of carbide is found to form at this temperature. Our results imply that new multilayer structures, e.g., compound multilayers will have to be developed for use at high temperatures or under high X-ray incident flux.