The influence of defects in nanograins, e.g. stacking faults and twinnings, on mechanical properties of nanocrystalline materials is studied by molecular dynamics simulations. Two types of many-body interatomic potential based on aluminium are adopted to investigate the influence of stacking fault energy on the deformation mechanism of nanocrystalline metals: one accurately reproduces the energy value of stacking faults for aluminium; the other underestimates the energy value for aluminium. Three different deformation processes are performed to nanocrystalline models with high or low stacking fault energy, and crystal slips occur in both models. In the case of the high stacking fault energy, crystal deformation occurs by perfect dislocations and no defects exist in the grains. Therefore, the strength almost recovers after relaxation. On the other hand, for low stacking fault energy, stacking faults remain through the grains after the crystal slips by partial dislocations. Consequently, these defects cause anisotropy in the mechanical properties of the simulated nanocrystalline metals.