At present, the theoretical predictions of the mechanical properties of transition-metal nitride (TMN) superlattices (SLs) are primarily based on the intrinsic properties of perfect epitaxial nanolayers. However, due to a lack of understanding of the specific strengthening mechanism, the experimentally determined strength, e.g., hardness, of TMN SLs often deviates significantly from the theoretical predictions. Here, by coupling FIB (focused ion beam) sectioning with TEM, we observe the structural evolution of two representatives TiN/AlN SL coatings, i.e., a single-crystalline and a polycrystalline SL, under identical loads. We found that in comparison with the polycrystalline SL, the indented single-crystalline SL forms a larger ‘intermixed’ region, within which the layer structure transforms into a solid solution under loads. Close TEM characterization demonstrates that the single-crystalline SL deformation is of variety, including the distortion of SL interfaces, polycrystalline deformation (grain rotation) in solid solution, and SL slip deformation. By contrast, columnar grain boundary sliding is the primary deformation mechanism in the polycrystalline SL. And, a relatively large solid-solution zone in single-crystalline SL is attributed to the severe interfacial deformation. The current research unravels TMN SL deformation behavior at the atomic scale.