We report a two-step process for the growth/patterning of Ni honeycomb nanostructures on various substrates, such as carbon paper, carbon nanotubes (CNTs), silicon wafers, and copper grids, via the combination of a sputter-coating/patterning technique and a replacement reaction solution method. The morphology, crystallinity, and chemical composition of the honeycombs were analyzed by SEM, TEM, high-resolution TEM, and EDX. These honeycombs are composed of numerous nanocells, several tens of nanometers in diameter and with cell wall thickness of approximately 10 nm, randomly connecting to each other. The growth process of honeycomb nanostructures has been systematically studied. Interestingly, the diameter and wall thickness of the cells could be easily tuned by simply adjusting the experimental parameters, such as the concentrations and cations of metal salts. Additionally, this simple method has been successfully extended to synthesize Co nanostructures with well-controlled morphologies, which indicates the great potential of this strategy in the synthesis of other metal nanostructures on various desired substrates. These metal-substrate composites, especially with desired patterns, are expected to be ideal candidates for wide application in modern electronic and optoelectronic devices, sensors, fuel cells, and energy storage systems.