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. I n recent years, efficient modulation of the thermal transport has become more and more urgent due to the imperative need to enhance the heat dissipation rate in the continuously miniaturized electronic devices and the acute demand to improve energy conversion efficiency based on thermoelectrics. Because phonons dominate heat transfer in crystalline dielectrics and semiconductors, the manipulation of the thermal conductivity (κ) can be realized through controlling phonons by two types of mechanisms: the incoherent phonon scattering mechanism and the coherent mechanism. Here the coherent mechanism means the manipulation of phonons via the modification of phonon dispersion arising from the phonon wave effects, such as the opening of phononic band gaps and the reduction of group velocity, which reflects the coherent nature of phonons. In contrast, the incoherent mechanism means to treat phonon scatterings similar to the particle collisions that originated from the diffusive phonon scatterings by the boundary, impurity, or intrinsic anharmonic phonon− phonon interaction. In this case, the coherence/correlation of phonons is lost, that is, the incoherent effect. Traditionally, the thermal conductivity is manipulated through impurities, 1,2 nanoparticles, 3−6 defects, 7−12 ion-inter-calation, 13 encapsulation, 14 interparticle constriction, 15 and static electricity 16 in materials by manipulating the incoherent phonon scattering. 17,18 Recently, a new strategy focuses on managing phonons by superlattice and nanostructured phononic crystals (PnCs), 4,19−28 which allows for controlling heat by engineering the phonon band structures (coherent phonon transport). 29−33 The coherent phonon transport behavior has been observed in several theoretical 34−36 and experimental 37−39 investigations on superlattice structures, such as in Si/Ge, 34 graphene/boron nitride, 35,36 and GaAs/