Hydrothermal stability is one of the major challenges facing heterogeneous catalysis in biomass conversion to chemicals or fuels. Though carbon supports have shown better hydrothermal stability than common metal oxide supports like alumina and silica, improving the stability of metal nanoparticles supported on carbon still remains a challenge. In this work, carbon-coated SBA-15 (mesoporous silica) materials in which thin carbon overlayers were pyrolyzed at 300, 400, and 600 °C giving different surface chemistries, as quantitatively verified by 13C NMR and XPS. As the pyrolysis temperature increased, the carbon overlayer had fewer oxygen functional groups and more aromatic groups. After depositing Pd nanoparticles on the support, hydrothermal treatments and aqueous-phase furfural hydrogenation were used to test the catalyst stability. Better Pd dispersion and enhanced hydrothermal stability were observed when Pd was supported on the carbon-coated SBA-15 pyrolyzed at lower temperature.