Bio-chemical molecular detection in the nanoscale, based on alloyed nanorods (NRs) with tunable surface plasmon resonance (SPR) properties and high chemical stability, has attracted particular interest. In this work, alloyed Au-Ag NRs with tunable aspect ratios were achieved by annealing Au nanobipyramid-directed Au@Ag core-shell NRs. The core-shell NRs were encapsulated within mesoporous silica outer shells to avoid fusion or aggregation. The structural stability of fully alloyed Au-Ag NRs, including chemical and thermal stability, is remarkably improved compared with that of Au@Ag core-shell NRs. The alloyed NRs would maintain the rod-like structure after being incubated in etchant solution, while Au@Ag core-shell NRs would decay into nanobipyramids. Additionally, fully alloyed NRs present stable morphology under annealing at high temperatures of up to 600°C in air. Benefiting from excellent structural and chemical stabilities, the surface-enhanced Raman scattering effect based on alloyed NRs is stable in harsh environments. Taking advantage of tunable SPR properties (600–1800 nm) and excellent stability, the obtained nanostructures can serve as drug carriers. The perfect photo-thermal effect induced by the particular SPR of alloyed NRs can improve the release efficiency of drugs.