Crystalline-amorphous nanolaminates represent a unique class of hierarchically structured materials where deformation is governed by a confluence of mechanisms deriving from defect interactions with both phase and grain boundaries. While a number of pioneering studies have shown that the amorphous layers act as both a source and sink for dislocations operating within the crystalline regions, design principles for simultaneously optimizing the multiple inherent structural length scales to tune plasticity at the nanoscale have yet to be established. Using molecular dynamics simulations, we first explore the influence of structural length scales including the crystalline-to-amorphous layer thickness ratio and nanocrystalline grain size on the underlying deformation mechanisms. Illustrative compound deformation mechanism maps capturing contributions from the three dominant mechanisms– shear transformation zone, dislocation, and grain boundary plasticity– are constructed to provide new insights into mechanistic transitions as a function of phase and interfacial volume fraction. Microstructural design windows are identified based on an Ashby plot analysis combining ductility-limiting localization factors with flow stresses calculated from the simulated stress-strain curves. Guided by the insights from atomistic simulations, nanocrystalline modulated Ni-W alloy nanolaminates are synthesized via electrodeposition and used to map mechanical properties including hardness and activation volume through nanoindentation. With the activation volume serving as a signature for the underlying deformation mechanisms, we correlate the measured mechanical properties to the deformation mechanism maps from atomistic simulations and identify microstructural conditions that produce a crossover to shear band dominated plasticity.