Several physico-chemical effects and properties in the solid state involve nanoscale interactions between adjacent materials and morphologies. Arrays of binary nanostructures can generate intimate interactions between different subcomponents, but fabricating binary nanostructures is challenging. Here, we propose a concept to achieve diverse binary nanostructure arrays with high degrees of controllability for each of the sub-components, including material, dimension and morphology. This binary nanostructuring concept originates with a distinctive binary-pore anodized aluminium oxide template that includes two dissimilar sets of pores in one matrix, where the openings of the two sets of pores are towards opposite sides of the template. Using the same growth mechanism, the binary-pore template can be extended to multipore templates with more geometrical options. We also present photoelectrodes, transistors and plasmonic devices made with our binary nanostructure arrays using different combination of materials and morphologies, and demonstrate superior performances compared to their single-component counterparts.