Through nonequilibrium molecular dynamics simulations, we report the direct numerical evidence of the coherent phonons participating in thermal transport at room temperature in graphene phononic crystal (GPnC) structure and evaluate their contribution to thermal conductivity based on the two-phonon model. With decreasing period length in GPnC, the transition from the incoherent to coherent phonon transport is clearly observed. When a random perturbation to the positions of holes is introduced in a graphene sheet, the phonon wave-packet simulation reveals the presence of notable localization of coherent phonons, leading to the significant reduction of thermal conductivity and suppressed length dependence. Finally, the effects of period length and temperature on the coherent phonon contribution to thermal conductivity are also discussed. Our work establishes a deep understanding of the coherent phonons transport behavior in periodic phononic structures, which provides effective guidance for engineering thermal transport based on a new path via phonon localization.