The mechanism of mercury (Hg) amalgamation in gold nanorods coated with a mesoporous silica shell (AuNRs@mSiO 2 ) and the effect of chemical treatments on the localized surface plasmon resonance (LSPR) spectral changes in single amalgamated AuNRs@ mSiO 2 remains unclear. In this study, we investigated Hg amalgamation and inward Hg diffusion in single AuNRs@mSiO 2 without structural deformation via dark-field scattering spectroscopy and X-ray photoelectron spectroscopy. Then, we investigated the chemisorption of thiol molecules on single amalgamated AuNRs@Hg-mSiO 2 . Unlike previous studies on single AuNRs, the thiolation on single AuNRs@Hg-mSiO 2 resulted in a redshift and line width narrowing of the LSPR peak within 1 h. To determine the chemical effect, we investigated the competition between two surface damping pathways: metal interface damping (MID) and chemical interface damping (CID). When we exposed amalgamated AuNRs@Hg-mSiO 2 to 1-alkanethiols with three different carbon chain lengths for 1 h, we observed an increase in the line width broadening with longer chain lengths owing to enhanced CID, demonstrating the tunability of CID and LSPR properties upon chemical treatments. We also investigated the competition between the two surface damping pathways as a function of the time-dependent Au−Hg surface properties in AuNRs@Hg-mSiO 2 . The 24-h Hg treatment resulted in increased line width broadening compared to the 1-h treatment for the same thiols, which was attributed to the predominance of CID. This was in contrast to the predominance of MID under the 1-h treatment, which formed a core−shell structure. Therefore, this study provides new insights into the Hg amalgamation process, the effect of chemical treatments, competition between surface decay pathways, and LSPR control in AuNRs@mSiO 2 .