Chemical enhancement in surface-enhanced Raman scattering (SERS) of pyrazine adsorbed on Au–Pd nanoclusters is investigated by using density functional theory. Changing Pd content in the bimetallic clusters enables modulation of the direct chemical interactions between the pyrazine and the clusters. The magnitude of chemical enhancement is correlated well with the induced polarizability for the complexes with low Pd content, which fails for the complexes with high Pd content. Furthermore, the dependence of chemical enhancement on cluster size and coupling is also described by the induced polarizability. Additionally, the chemical enhancement in the cluster–molecule–cluster junction is found to account for as much as 103, which suggests that a chemical mechanism might be more important than previously believed, in particular for Au–Pd bimetallic nanoparticle aggregates.