Building nanoparticle (NP) superlattices formed in a complex fashion by subsets that can be explored separately presents a promising approach to realize the next generation of superlattices for different applications. Here, by incorporating self‐aligned and geometrically different subsets of Au NPs into one matrix with the assistance of multi‐pore anodic alumina oxide templates, scaled‐up NP superlattices are constructed with programmable multiple plasmonic resonances. The inter‐peak spectral distance is tailored in a broad wavelength range from less than 50 nm up to about 1000 nm through altering not only the size and height of each subset, but also the number and nature of the NP subset. Importantly, a mechanical oscillator model is developed to elucidate the microscopic origin of the spectral programmability and to reproduce the parameter dependence of the multiple plasmonic resonances. A photoelectrochemical cell using Au NP superlattice embedded photoanodes is investigated as a proof‐of‐concept, demonstrating a high photoresponse improvement of about 260% compared to that of bare film reference. In light of the compatibility of this technique with other plasmonic materials and the geometrical tunability, these findings enable systematic optical controlling toward optical devices with multimodal plasmonics.