Nanocrystalline metals exhibit many excellent mechanical properties and their underlying deformation mechanisms have been studying widespread. The well-designed atomistic simulations can predict the mechanical behavior of materials ahead of experiments and provide sufficient information on the atomic scale. The choice of appropriate interatomic potential is one of the main concerns of any atomistic simulation that needs to be seriously considered in order to obtain reliable results. In this study, we investigated the mechanical response and the deformation mechanisms of nanocrystalline Al under uniaxial loading by molecular dynamics (MD) simulations with different embedded atom method (EAM) interatomic potentials. The selection of potential has a significant influence on the simulation result, and the reliability of these potentials was evaluated based on the available experimental data in the literature. In the elastic stage, the stress-strain response and Young's modulus of the simulated samples varied with different potentials. Three independent elastic constants of single crystal Al were used to predict the isotropic elastic modulus of the polycrystal Al sample. In the plastic stage, multiple grain boundary (GB) induced deformation mechanisms were observed, including GB migration, intergranular fracture, dislocation nucleation from GB, and deformation twinning. The generalized stacking fault energies of Al were calculated by MD simulation using different potentials, and their effects on the dislocation nucleation and deformation twinning mechanisms were discussed. This work signifies the important role of GBs play in nanocrystalline metals during plastic deformation and highlights the significance of using the appropriate interatomic potential for a specific simulation problem.