Commonly obtained SBA-15 particles (fiber-like morphology), if used as a catalyst-host, has limitations in diffusion of reactant molecules (e.g. of a dye) inside the pores of the SBA-15 particle. The systematic synthetic approach developed here provides an easy control of SBA-15 particle morphology over a wide range (fiber, rod, and sphere), by only varying the HCl concentration. To assess its effect on molecular diffusion and reaction inside pores, SnO₂ nanoparticles of 3.5 nm diameter were synthesized in situ, inside the 6.3 nm diameter pores of SBA-15. These hybrids were tested for photocatalytic degradation of rhodamine B dye. Sphere-like morphology of SBA-15 with SnO₂ nanoparticle loading of 17.7 wt% showed the highest first-order degradation rate constant of 0.54 h⁻¹, compared to other morphologies (rod—0.51 h⁻¹, fiber—0.33 h⁻¹). On incorporating rates of diffusion, adsorption, and degradation-reaction of the dye in a single pore-level mathematical model of the SBA-15 particle, we have predicted the experimentally measured temporal variation of dye concentration for different SBA-15 morphologies and SnO₂-catalyst loadings. Therefore, the present work identifies the best SBA-15 particle morphology (sphere-like) for such reactions and provides a validated model to optimize such coupled problems of chemical transport and reaction.