Pickering emulsions offer a promising platform for conducting interfacial reactions between immiscible reagents. Despite the significant progress in the engineering of amphiphilic catalysts for such reactions, the mechanism behind their enhanced activity is still poorly understood. Herein, using the glycerol/dodecanol system as a case study, we conducted a combined meso- and microscale study of Pickering emulsions stabilized by amphiphilic silica nanoparticles bearing acid centers by marrying dissipative particle dynamics simulations with emulsification experiments. The optimal surface properties of the silica particles in terms of length and density of alkyl chains were identified, matching the experimental results. The local distribution of glycerol and dodecanol near the acid centers was ascertained, unraveling potential reactivity zones near the catalytic acid centers due to an enhanced nanomixing between glycerol and dodecanol.