The characterization of wear response in crystalline materials poses some challenges due to the presence of the size effect at small scales. In this study, we systematically conducted spherical nano-scratch simulations on (101)-oriented copper, using the mechanism-based strain gradient crystal plasticity theory, to explore the indenter size effect in the scratch hardness. The developed nano-scratch models are validated experimentally by comparing scratch depths and topographies. By examining the results obtained from conventional crystal plasticity and mechanism-based strain gradient crystal plasticity simulations, an indenter size effect in scratch hardness was identified. Furthermore, the mechanism of the indenter size effect in scratch hardness was quantitatively analyzed, by discussing the proportion of geometrically necessary dislocation lengths in the cumulative increments of dislocations.