Stabilizing non-equilibrium nanograin boundaries has been shown to enhance the strength of nanocrystalline metals. Nevertheless, a thorough comprehension of how these stable grain boundaries impact the fatigue behavior in nanocrystalline metallic layered composites with heterogeneous interfaces is currently lacking. Here, aiming to develop high-performance small components in microelectromechanical systems, we prepared nanocrystalline Ni/Ni-W layered composites that underwent various degrees of annealing treatment. Our results reveal that the Ni/Ni-W layered composites annealed at 200 °C exhibit significantly higher fatigue strength, surpassing that of the as-prepared composites by 40 % and the Pt-10 at.% Au alloy by 17 % which is one of the best candidates for the microelectromechanical systems switches at present. The enhanced fatigue strength is primarily attributed to the annealing-induced grain boundary relaxation and mechanically-induced structural relaxation. Grain boundary relaxation enhances the strength by improving GB stability, while the mechanically-induced structural relaxation results in the coarsening and expansion of triangular columnar grains towards the Ni-W layer during fatigue loading. As a result, the dispersive strain localized regions triggered by the triangular columnar grains undertook cyclic strain accumulation and weakened localized damage accumulation in Ni layers, and thus further improved the fatigue resistance. The finding of the underlying mechanisms may offer a promising approach for designing high-performance materials for microelectromechanical systems switches operating at elevated temperatures.