The ability to control nanoparticle size, concentration, and distribution in epitaxial nanocomposite films has been a formidable challenge in the synthesis of nanostructured composite materials. Here, a novel 3D supernanocomposite (3D-sNC) architecture is successfully demonstrated by integrating superlattice and vertically aligned nanocomposite structures. In the 3D-sNC architecture, the feature size and distribution of the nanocylinders such as the height/lateral dimension and the vertical/lateral spacing of nanocylinders can be precisely controlled. The microstructure parameters such as nanocylinder height and spacing modulated interfacial area control the lattice strain, which further tunes the magnetotransport property. These results demonstrate that 3D-sNC is a simple and yet effective architecture to achieve controlled functionalities via the precise control of nanocylinder size, spacing, concentration, and distribution. Such a 3D-sNC structure can be used to design advanced nanostructures with desired physical properties for a variety of material systems.