Incoherent twin boundaries (ITBs) can significantly affect the mechanical properties of twin-structured metals. However, most previous studies have focused on the deformation mechanism of the coherent twin boundary (CTB), and metals with ITB-accommodated plasticity still require further investigation. In this study, deformation mechanisms of FCC-structured nanocrystal metals with ITBs were investigated using molecular dynamic (MD) simulations. We revealed that three deformation mechanisms occur in metals with ITBs. The first type of deformation was observed in Au, where the plasticity is governed by partial dislocation intersections with CTBs or reactions with each other to form Lomer–Cottrell (L–C) locks. In the second type, found in Al, the deformation is governed by reversible ITB migration. The third type of deformation, in Ni and Cu, is governed by partial dislocations emitted from the ITB or the tips of the stacking faults (SFs). The observed L–C lock formation, as well as the reversible ITB migration and partial dislocation emission from the tips of SFs, have rarely been reported before.