Precise organization of nanoparticles (NPs) into regularly well-defined arrays represents a continuing challenge in the development of high-performance metamaterials. Herein, zone-annealed diblock copolymers provide an effective medium for construction of periodically well-ordered arrays of NPs within mechanically enhanced nanocomposites. By integrating the dynamic self-consistent field theory for diblock copolymers and molecular dynamics for NPs, it is revealed that the emergence of response layers of asymmetric diblock copolymers induces the epitaxial assembly of NPs during the processing of hot zone annealing. In particular, the ability to kinetically control the assembly pathway of NPs enables them to be organized into hexagonally packed, defect-free arrays, with essentially the individual NP in a unit cell. Our simulations also show that the moving speed of annealing fronts and the concentration and radius of NPs all play important roles in engineering both the spatial arrangement and organization of NPs in a diblock copolymer matrix. Furthermore, the information from the simulations of diblock copolymer/NP mixtures is used to deduce mechanical responses of polymeric nanocomposites by the lattice spring model. The results reveal that the spatial arrangement and organization of NPs in the diblock copolymer matrix provide additional reinforcing elements to enhance the strength of structural materials. Merging the self-assembly of nanocomposites with the zone annealing processing can provide a means of kinetically controlling the assembly pathway for the achievement of regularly well-ordered arrays of polymer-embedded NPs with structural and optoelectronic functionalities.