Pickering emulsions stabilized by solid catalysts have received an increasing amount of attention as a reaction platform because of potential applications in the chemical industry. Here, we report a surface modification strategy for controlling the catalytic performance of Pd/Al2O3 during vanillin hydrodeoxygenation (HDO) in a water/decalin emulsion environment. A series of organophosphonic acids (PAs) were applied as modifiers to control the surface hydrophobicity, thereby determining the continuous and dispersed emulsion phases. The PAs also introduced Brønsted acid sites that promoted vanillin HDO. Reaction studies showed that the yield of the HDO product p-creosol was improved from 20% to as high as 90% upon PA modification after a reaction duration of 1 h at 50 °C. This improvement greatly depended on the surface hydrophobicity, which influenced the selectivity to different reaction pathways as well as the emulsion structures. Statistical analysis of the kinetic data confirmed the hydrophobic/hydrophilic effect.