Growth of N-polarity GaN on a two-dimensional (2D) material is of significance for the development of high-performance nitride devices such as red light-emitting diodes. However, the realization of N-polarity GaN on a 2D material is a challenge. In this work, we successfully achieve N-polarity GaN on graphene/SiC substrates through interfacial atomic manipulation. Our results show that the growth conditions of the AlN buffer play an important role in the lattice polarity of nitride film grown on 2D graphene. A low growth temperature of AlN buffer leads to a metal-polarity nitride film, while a high growth temperature of it leads to a mix-polarity nitride film. The underlying mechanism is revealed by first-principles calculations. Under the guidance of the calculations results, the preflow of trimethylaluminum source is introduced prior to the high-temperature AlN buffer growth to manipulate the interfacial atoms between the AlN buffer and graphene/SiC. With this method, we successfully realize the fabrication of N-polarity GaN on graphene/SiC by metalorganic chemical vapor deposition. This work provides a new route for the development of high-performance N-polarity nitride devices on graphene/SiC substrates.