The figure shows the physical property of Cu47.5Zr47.5Al5 alloy in the various structures: polycrystalline (a) and twinned polycrystalline (b). Display omitted •GB and TB play a significant role in preventing the spread of deformation.•High stress is located in front of the indenter and in the vicinity of GB.•Plastic deformation is governed by the interaction of dislocation-GB-TB.•The inverse Hall-Petch relationship is observed with different grain sizes. Molecular dynamics (MD) simulation is applied to study the plastic deformation response of the nanoscratching process via the investigation of an indenter sliding on the surface of CuZrAl nanocrystalline. The effects of different crystal structures, alloy compositions, grain sizes, and twin lamellar thicknesses are paid special attention. The results show that the force and hardness are decreased in the order of single crystalline, twinned polycrystalline and polycrystalline. The average force value during the scratching stage is larger when the Cu content decreases. Interestingly, the inverse Hall-Petch relationship is observed from the change of grain sizes and twin lamellar thicknesses. Furthermore, the grain boundary (GB), twin boundary (TB) and grain growth play a significant role in preventing the spread of deformation in the polycrystalline and twinned polycrystalline structures. The plastic deformation of single crystalline is controlled by the interaction of dislocations. Whereas the plastic deformation of polycrystalline is dominated by the interaction of dislocation and GB. For twinned polycrystalline, the interaction of dislocation-GB-TB has simultaneously occurred in the deformation process. A comparison of the special wear rates, this value is the largest with the polycrystalline structure in different crystal structures, while it tends to rise as decreasing the grain size.