<p>This study utilizes molecular dynamics (MD) simulations to develop a cyclic nanoindentation framework and to examine the deformation responses of single-crystal and nano-polycrystalline NiAl shape memory alloys (SMAs) subjected to cyclic loading and unloading. The influence of peak indentation load and grain size on cyclic deformation is systematically evaluated, and the microstructural mechanisms underlying progressive cyclic degradation during successive indentation cycles are clarified. The results indicate that pronounced plastic deformation occurs in the first loading cycle and the hysteresis loops of the load–displacement response decrease progressively in subsequent cycles. The residual indentation depth increases monotonically with increasing peak load or decreasing average grain size. For single crystal NiAl SMAs, the cyclic deformation mechanism is governed by the accumulation of residual martensite, stacking faults, and disordered atomic structures. In nano-polycrystalline NiAl SMAs with a grain size of 4 nm, the accumulation of residual depth is mainly attributed to stacking faults, disordered structures, and plastic deformation in grain boundary regions. By contrast, the combined effects of residual martensite, stacking faults, disordered structures, and grain boundary-mediated plastic deformation are responsible for the residual depth accumulation in SMAs with grain sizes of 8 nm and 12 nm.</p>