The widely observed non-diffusive phonon thermal transport phenomenon in nanostructures is largely attributed to classical size effects, which ignore the characteristic of phonon wave. In this context, the crossover transition process from incoherent to coherent phonon transport in two-dimensional heterogeneous periodic h-GaN/h-AlN superlattices is demonstrated using a non-equilibrium molecular dynamics approach, where the localization behavior of thermal phonons is particularly significant. The results show that the thermal transport of the superlattice structure is affected by a combination of structural parameters and temperature. The thermal conductivity (TC) of the superlattice decreases and then increases as the interface density increases. Phonon-interface scattering dominates the incoherent phonon transport, while local phonons modulate the transport in the coherent region. Thus, the competition between phonon wave and particle properties causes the transition from incoherent to coherent phonon transport. In addition, as the TC valley depth slows down with increasing system temperature, the scattering of medium and high frequency phonons is enhanced and the phonon lifetime decreases. Research on localized phonons in superlattices provides theoretical support for thermal transport regulation in basal low-dimensional materials.