Silica aerogels are nanostructured materials known for their low density, high porosity, and excellent thermal insulation properties. Among silica aerogels, organosilane‐derived aerogels have received considerable interest for their additional chemical functionalities such as hydrophobicity and flexibility. This work investigates the mesoscopic modeling of such aerogels, extending an aggregation based model developed for conventional silica aerogels. The pH of sol–gel polymerizations is one of the most critical reaction and processing parameters in determining the porosity, density, strength, and transparency of the resulting gels. Achieving optical transparency in aerogels depends on the presence of homogeneous mesoporous network structures. To account for the effect of pH, a relationship between pH and adhesion probability was incorporated into a three‐dimensional cluster‐cluster aggregation (CCA) model, providing insight into the gelation process. In addition, size‐dependent diffusivities are considered in this study. By incorporating different factors into the CCA model, the gelation kinetics are evaluated. The obtained mesoscopic structure is compared with experimental characterizations, together with preliminary mechanical simulations.