Engineering the surface plasmon resonance (SPR) properties is a critical issue for improving device performance in the fields of plasmonics, nanophotonics, optoelectronics, and electrochemistry. Here, we demonstrated a programmable manipulation of the surface plasmon resonance (SPR) effect using composition-adjustable Ag-Au substitutional alloy microcages (SAMCs) through a facile NaBH4-cooperative galvanic replacement reaction. The SPR frequency of the Ag-Au SAMCs can be continuously and exquisitely manipulated without resonance damping or broadening via accurate adjustment of the elemental composition distribution at the perfect homogeneity on the atomic-level. Significantly, both the tunable SPR frequency and excellent chemical stability synergistically endow the hollow Ag-Au SAMCs with excellent SERS sensitivity and reproducibility, which lays a foundation for the realization of trace detection of thiram at an ultralow concentration of 1 × 10-12 M. This strategy is a promising candidate for efficient promotion of the SERS activity for metal-based substrates.