A heterostructure film composed of graphene and h-BN has superlubricity and long-term anti-corrosion performance, enabling its potential applications as low-friction and corrosion-resistant coatings, especially in marine environments. However, the grain boundaries (GBs) and point defects formed during the preparation process may significantly affect the performance of the film. In this study, the tribological properties and wear mechanism of heterostructure films with different GB misorientation angles were studied with the molecular dynamics method. The results show that the high-energy atoms generated by strain-induced hillocks along the GBs can lead to stress concentration, thus deteriorating the wear resistance of the heterostructure film. Furthermore, point defects occurring on high-energy atoms can significantly alleviate the stress concentration, which is conducive to improving the wear resistance of the film. This study sheds light on improving the tribological characteristics of a graphene/ h-BN heterostructure coating by properly controlling its microstructure.