Heterostructures with multiple strongly coupled quantum wells, such as super-multiperiod (SMP) superlattices (SLs), are promising semiconductor devices, which may contain hundreds or even thousands of layers with 100 or more periods synthesized by molecular beam epitaxy (MBE) to high structural perfection. The proposed characterization method employs matched application of high-resolution x-ray diffractometry (XRD), reflectometry (XRR), and, for the first time, the deep XRR (DXRR) allows the study of SMP structures, as well as high-accuracy determination of the thicknesses of layers, roughness/diffuseness of boundaries using the rigorous scattering theory, and composition of solid solutions. Combining these methods with scanning transmission electron microscopy (STEM) enables characterization of SMP SLs and independent determination of these same parameters. The differences between the expected and obtained layer thicknesses by XRD and XRR were 1%-3% for AlGaAs/GaAs structures. The samples were characterized by sharp interfaces with the root-mean-square width of the transition layers of the order of a few angstrom, which is consistent with the XRR/DXRR and STEM analysis. Based on the data obtained for the thicknesses of layers, the composition of Al0.3Ga0.7As has been accurately determined by the x-ray methods. These results may be considered as the first step in the analysis of MBE-grown SMP structures with a number of periods up to 1000.