The multilayer nanostructures have drawn attention in fields from spintronics to microwave electronics. The purpose of this work was to determine the composition of individual layers and to control interfaces in three‐layer superstructures [(Co40Fe40B20)34(SiO2)66/ZnO/C]46 by means of X‐ray diffraction and X‐ray reflectivity. The samples with different thicknesses of metal‐containing composite layers together with zinc oxide and carbon interlayers were deposited on the glass substrate by ion‐beam sputtering of three targets, one of which was a composite (Co40Fe40B20)34(SiO2)66. X‐ray diffraction results showed the X‐ray amorphous state of the ferromagnetic metal clusters CoFeB, the dielectric matrix of silicon oxide SiO2, and carbon interlayers. However, the intermediate layers of the zinc oxide ZnO were found to have a nanocrystalline structure. The X‐ray reflectivity measurements indicate a good agreement between the experimental and nominal values of both the periods of three‐layer superstructures and the thicknesses of metal‐containing composite layers and interlayers.