Scale dependent microstructures and plastic deformation in Ni/Al nanomultilayers with different modulated ratio has been investigated as a function of bilayer thickness by X-ray diffraction and nanoindentation. Experimental results show that the hardness and the related microstructural parameter in the softer sublayer exhibited the similar variation tendency, which indicated the sensitivity of plastic behaviors on the microstructural constraints in softer sublayer. Further investigation showed that in the nanometer regime, by adopting a new parameter r in softer sublayer (r=Lsub/d, where Lsub is the sublayer thickness and d is the grain size), the competing grain-boundary and interface-boundary strengthening mechanisms could be unified. Moreover, within the overall scale, the deformation of nanomultilayers could follow the Hall-Petch relation with decreasing characteristic length scales.