We study the processes of dynamical diffraction on the graphene film/SiC substrate system. The statistical dynamical theory of X-ray diffraction in imperfect crystals is extended to the case of real quasi-two-dimensional systems. The necessity of the taking into account of the variability of the lattice parameter of multilayer graphene, as well as the influence of thickness on the thermal Debye–Waller factor at the calculation of the complex structural factors and Fourier components of polarizability, is demonstrated. It is shown that the change of the structural characteristics of the 3-layer graphene/substrate system, as well as its deformed state, leads to a significant change in the diffraction profiles, which makes it possible to determine the characteristics by the X-ray diffraction method.