Ni-based multilayered film is attractive due to its high good thermal conductivity, oxidation resistance and mechanical properties. However, the influence of individual layer thickness on the microstructure thermal stability and mechanical properties have seldom been investigated. Hence, the 5 at.% Mo and 5 at.% W co-added in Ni/NiAl multilayers with individual layer thicknesses ranging from 10 nm to 160 nm were synthesized using co-sputtering. Upon post-annealing at 600 °C, the phase separation of γ-Ni solid solution in multilayer occurs, precipitating dispersed nano-sized α-W phases in major when individual layer thicknesses are lower than 40 nm. The periodical layer interfaces of these multilayers are maintained with excellent thermal stability. The hardness of multilayer is enhanced with reduction of individual layer thicknesses due to grain boundary relaxation, increased layer interfacial barriers and W-related precipitations as obstruction for dislocations movement, showing anneal hardening significantly. Due to crack deflection at the layer interfaces, less brittle W-relative phase precipitation and bare columnar crystals growth, the superior toughness is achieved for 600 °C annealed multilayer with individual layer thicknesses of 40 nm. Therefore, 5 at.% MoW co-alloyed Ni-based multilayer are suitable for high-temperature applications with excellent mechanical properties by modulation of individual layer thicknesses.