Graphene/hexagonal boron nitride (h-BN) van der Waals (vdW) heterostructure has aroused great interest because of the unique Moiré pattern. In this study, we use molecular dynamics simulation to investigate the influence of the interlayer rotation angle θ on the interfacial thermal transport across graphene/h-BN heterostructure. The interfacial thermal conductance G of graphene/h-BN interface reaches 509 MW/(m2K) at 500 K without rotation, and it decreases monotonically with the increase of the rotation angle, exhibiting around 50% reduction of G with θ = 26.33°. The phonon transmission function reveals that G is dominantly contributed by the low-frequency phonons below 10 THz. Upon rotation, the surface fluctuation in the interfacial graphene layer is enhanced, and the transmission function for the low-frequency phonon is reduced with increasing θ, leading to the rotation angle-dependent G. This work uncovers the physical mechanisms for controlling interfacial thermal transport across vdW heterostructure via interlayer rotation.