Graphene has shown excellent tribological behaviors, enabling its potential applications as lubricating and anti-wear coatings, however, the grain boundaries (GBs) formed during the preparation process may deteriorate the performance of graphene. Using large-scale molecular dynamics simulations, we study the wear mechanism of graphene GBs with various misorientation angles between two grains. Compared with pure nanoindentation at the GBs, the critical load of wear failure upon nanoscratching across the GBs is much lower due to the synergetic actions of interlocking and pushing between the tip and graphene atoms. The misorientation angle between the adjacent grains significantly effects the onset and fashion of atomic-scale wear. Results show that wear resistance of the graphene with large-angle GBs is slightly lower than that of pristine graphene. Nevertheless, a number of the long bonds emerge in the vicinity of the low-angle GBs during scratching, leading to wear failure at much smaller load than the large-angle GBs. Furthermore, wear resistance of the low-angle GBs can be enhanced by increasing the interfacial strength between graphene and substrate due to the reduced number of the long bonds at the GB. This study sheds light on improving wear resistance of graphene coating by properly controlling its microstructures.