We demonstrate the epitaxial growth of nitride heterojunction structures on two-dimensional materials. The growth behavior of Al atoms on hexagonal boron nitride (h-BN) involves preferential adsorption and diffusion along the N-top position, considerably improving AlN formation in the early stage of nucleation. Preferential N adsorption enables h-BN to provide a natural N surface for the substrate. Moreover, the natural N surface provided by h-BN can induce three-dimensional island-like order merging of the upper AlN layer, promoting dislocation slip annihilation. The dislocations annihilation depth of GaN films was shortened to 870 nm, resulting in an order of magnitude decrease in the density of screw dislocations to 5.50 × 107 cm−2 and considerable improvement in the performance of HEMT devices on SiC. Therefore, h-BN films can be used as two-dimensional insertion layers to obtain high-quality van der Waals epitaxial nitride films in GaN-based HEMT devices.