The structure of GaN/AlN heterointerface is commonly used in the high electron mobility transistors. To investigate the evolution and influence of GaN/AlN heterointerface during thinning, the grinding process of GaN films is simulated by molecular dynamics. The differences in the grinding process between GaN film with different thickness and pure GaN are compared. It is found that dislocation and phase transformation are the main defects at the GaN/AlN heterointerface, which will cause the stress concentration in the workpiece. The thinning process will lead to the evolution of the heterointerface and reduce the dislocation at the interface. Compared with the thinning of pure GaN, the heterointerface will promote the transformation from hexagonal wurtzite structure to cubic zinc-blende structure. In addition, there will be more chip atoms in the thinning process, because the heterointerface can hinder heat conduction and result in the higher temperature of GaN film.