The design and fabrication of core–shell and yolk–shell nanostructures with surface plasmon resonance (SPR)-active center protected by permeable mesoporous channels can raise the new vitality into the catalysis and biological applications. Hybrid plasmonic-mesoporous silica nanocarriers consisting of Ag and Au–Ag alloy nanoparticles are fabricated through spatially confined galvanic replacement approach. The plasmonic absorption peaks can be finely controlled to the near-infrared (NIR) region (500–790 nm) that is beneficial for tissue transmittance. The mesoporous silica shell facilitates also protection of Au–Ag cores and affords the channels between the exterior and interior capsule environments, thereby endowing the multiple applications. In the present work, it is successfully demonstrated that mesoporous silica-coated Au–Ag alloy core–shell and yolk–shell nanocarriers can serve as good substrates for surface-enhanced Raman scattering (SERS) detection. The SERS signal intensities of nanocarriers are highly dependent on the SPR peaks and the contents of gold. Simultaneously, the synthesized Au-Ag@mSiO₂ nanocarriers with SPR peak at ≈790 nm can be applied in NIR-sensitive SERS detection and photothermal therapy.