The thermoelectric properties of in-plane heterostructures made of Graphene and hexagonal boron nitride (BN) have been investigated by means of atomistic simulation. The heterostructures consist in armchair graphene nanoribbons to the sides of which BN flakes are periodically attached. This arrangement generates a strong mismatch of phonon modes between the different sections of the ribbons, which leads to a very small phonon conductance, while the electron transmission is weakly affected. In combination with the large Seebeck coefficient resulting from the BN-induced bandgap opening or broadening, it is shown that large thermoelectric figure of merit ZT > 0.8 can be reached in perfect structures at relatively low Fermi energy, depending on the graphene nanoribbon width. The high value ZT = 1.48 may even be achieved by introducing appropriately vacancies in the channel, as a consequence of further degradation of the phonon conductance.