This paper describes how the ability to tune each nanoparticle in a plasmonic hetero-oligomer can optimize architectures for plasmon-enhanced applications. We demonstrate how a large-area nanofabrication approach, reconstructable mask lithography (RML), can achieve independent control over the size, position, and material of up to four nanoparticles within a subwavelength unit. We show how arrays of plasmonic hetero-oligomers consisting of strong plasmonic materials (Au) and reactant-specific elements (Pd) provide a unique platform for enhanced hydrogen gas sensing. Using finite-difference time-domain simulations, we modeled different configurations of Au–Pd hetero-oligomers and compared their hydrogen gas sensing capabilities. In agreement with calculations, we found that Au–Pd nanoparticle dimers showed a red-shift and that Au–Pd trimers with touching Au and Pd nanoparticles showed a blue-shift upon exposure to both high and low concentrations of hydrogen gas. Both Au–Pd hetero-oligomer sensors displayed high sensitivity, fast response times, and excellent recovery.