This work investigates interfacial thermal transport in phononic‐mismatched heterostructures that consists of pristine black phosphorene and its phononic crystal. It is found that the presence of the sub‐periodic structure results in reduced thermal conductivity in phononic crystals. As opposed to intuitive expectations, a slight temperature jump is observed at the interface of nanophononic heterostructures, which is only about 10% of that at conventional interfaces consisting of dissimilar materials. Consequently, contact thermal conductance in the nanophononic heterostructure is 10−30 times higher than that of mass‐mismatched interfaces in a comparative study. Moreover, in contrast to conventional heterostructures achieved by interfacing dissimilar materials, weak temperature dependence is observed in interfacial thermal conductance, and thermal rectification is sharply suppressed. These phenomena are well explained based on lattice dynamic insights. This work not only enhances the understanding of the fundamental physics of phonons transport across interface, but also facilitates the possible spectrum of application ranges from thermoelectrics, thermal management, to thermal cloak. As opposed to intuitive expectation, a slight temperature jump is observed at the interface of nanophononic heterostructures, which is about 10% of that at the interface of dissimilar materials. Consequently, its contact thermal conductance is 10−30 times higher than that of mass‐mismatched interfaces. This work enhances the understanding of phonon transport, and facilitates the possible spectrum of application ranges from thermoelectrics, thermal management, to thermal cloaks.