The influences of different kinds of phonon scatterings (i.e., acoustic (AC) phonon, impurity, and longitudinal optical (LO) phonon scatterings) on the tunable propagation properties of graphene metamaterials structures have been investigated, also including the effects of graphene pattern structures, Fermi levels, and operation frequencies. The results manifested that, at room temperature, AC phonon scattering dominated, while with the increase in temperature, the LO phonon scattering increased significantly and played a dominate role if temperature goes beyond 600 K. Due to the phonon scatterings, the resonant properties of the graphene metamaterial structure indicated an optimum value (about 0.5–0.8 eV) with the increase in Fermi level, which were different from the existing results. The results are very helpful to understand the tunable mechanisms of graphene functional devices, sensors, modulators, and antennas.