The effect of twist angle on the hydrogenation of bilayer graphene (BLG) is systematically explored by density functional theory (DFT) calculations. We found that a twist between the upper and lower layers of the graphene BLGs, either big or small, interferes with the formation of inter-layer C–C covalent bonds and this leads to strong resistance to hydrogenation. In addition, the electronic properties of stable, hydrogenated twisted BLG with different twist angles and degrees of H coverage were investigated. This study paves the way to the selective functionalization of BLG for various applications.