The surface functionalization of silica nanoparticles (SiNPs) to enhance their compatibility and miscibility in the organic medium of bitumen has been performed using various coupling agents. 3-Aminopropyl triethoxysilane (APTES) and 3-glycidyloxypropyl trimethoxysilane (GPTMS) are among the effective silanization coupling agents; their successful performance is attributed to the unique properties imparted by their bifunctional characteristics. Here we study the interaction mechanisms controlling the silanization process that lead to the distinct performances of APTES and GPTMS in a bitumen matrix. On the basis of density functional theory results, the protonated amines (−NH3+) of APTES show a considerable interaction energy with Si surface silanols (−55.2 kcal/mol). The strong binding of APTES' amine head to the silica surface makes the silanols of APTES available for covalent condensation with surface silanols of the neighboring SiNPs or for self-condensation with free unreacted APTES molecules, promoting the agglomeration of the particles in a high loading of APTES. Compared with APTES, the lower aggregation in GPTMS-treated SiNPs can be attributed to the lower adsorption tendency of GPTMS' epoxy head to the available silanols, in particular, when the epoxy rings are not opened under the experimental conditions. The lower agglomeration in GPTMS-treated SiNPs leads to their smaller particle size. This was also evidenced in the larger surface area of GPTMS-treated SiNPs compared with APTES-treated SiNPs, as measured by inverse gas chromatography. It was further shown that the dual functionality of silane coupling agents allows them to bridge SiNPs to bitumen components. In the GPTMS case, nucleophilic centers of the asphaltene or resin molecules, such as −OH or −NH, attack the electrophilic carbons of epoxide at the position least hindered to create chemical bonds between the two species. In the APTES case, protonated amines can form ion-pair compounds through interactions with basic sites of bitumen, such as quinoline or pyridine resins. The lower agglomeration of the GPTM-treated SiNPs further manifested itself in a higher complex modulus for bitumen specimens containing APTES-treated SiNPs (4800 kPa) compared with bitumen containing GPTM-treated SiNPs (4.8 kPa) when measured at 1 rad/s and 40 °C.