Thermoelectric properties of graphene nanoribbons with periodic edge vacancies and antidot lattice are investigated. The electron-phonon interaction is taken into account in the framework of the Hubbard-Holstein model with the use of the Lang-Firsov unitary transformation scheme. The electron transmission function, the thermopower and the thermoelectric figure of merit are calculated. We have found that the electron-phonon interaction causes a decrease in the peak values of the thermoelectric figure of merit and the shift of the peak positions closer to the center of the bandgap. The effects are more pronounced for the secondary peaks that appear in the structures with periodic antidot.