A method has been proposed for the simulation of the atomic structure of disordered phases of nonstoichiometric transition metal oxides, carbides, and nitrides with the B1 structure taking into account the short-range order in the arrangement of structural vacancies. The simplest structural models constructed with allowance for pair correlations between vacancies within the first four coordination spheres have been considered. A computer simulation of the atomic structure of disordered phases with the inclusion of the short-range order has been performed. For each structural model, the maximum possible concentration of vacancies and the short-range order parameters at different concentrations have been calculated. For a further experimental verification, the influence of the short-range order on the shape of the X-ray scattering spectrum has been investigated by calculating the theoretical X-ray diffraction patterns according to the Debye formula. The influence of the short-range order on the total energy of the disordered phases has been analyzed by ab initio methods. It has been shown that, in some cases, the proposed structural models of the short-range order are energetically favorable as compared to the model of statistical arrangement of vacancies.