Nanoindentation simulations on flat and stepped surfaces are respectively investigated using the quasicontinuum method based on the embedded-atom method potential. Effect of surface step considering indenter size and step height is studied. Results show that the critical load for the first dislocation emission will be decreased with the increase of step height. However, the effect of surface step will be weakened if the indenter size continues to increase. Initial atomistic structures after dislocation nucleation and emission are discussed systematically. The initial dislocations are not quite identically nucleated under the stepped surface. Stress distribution analysis reveals that the shear stress in the slip planes close to the step is much larger than the shear stress in the slip planes far from the step for nanoindentation on the stepped surface. The multiscale simulation results are consistent with experimental results and analytic solutions. The conclusions about step effect considering indenter size and step height are helpful for understanding the microscopic mechanism of nanoindentation tests on thin films with surface step. (c) 2012 Elsevier B.V. All rights reserved.