Heterogeneous multilayer configurations are discussed to enhance plasmonic hydrogen sensors (PHSs). Five sensor designs─pure Pd, Pd/Ag, Ag/Pd, Ag/Pd/Ag, and Pd/Ag/Pd─were developed by sequentially depositing Ag and Pd on nanosphere arrays. The Pd/Ag/Pd configuration demonstrated maximum 10, 2.7, and 1.69 times superior performances in rapid hydrogen sensing, signal detection, and reduced limit of detection (LOD) compared to pure Pd sensors. The impact of material composition, ambient interactions, intermaterial coupling, and surface morphology on sensitivity and response time was quantitatively analyzed using one-hot encoding and linear regression. Finite-difference time-domain (FDTD) calculations were employed to reveal the near-field surface plasmon resonance (SPR) effects. This study would offer theoretical insights and guiding principles for future PHS advancements, particularly in enhancing sensor performance through a heterogeneous multilayer configuration.