Au9 nanoclusters (Au9 NCs) were deposited onto S-functionalized mesoporous TiO2 (SMTiO2) to produce efficient photocatalysts for Methyl Orange (MO) dye degradation with UV light. The morphology, the surface composition and the size of the deposited Au9 NCs of the catalyst was analysed. SMTiO2 could adsorb more clusters with lesser Au9 cluster agglomeration than unmodified MTiO2. This finding is attributed to the capability of the thiol groups to form strong bonds with the Au9 clusters. To study Au9 NCs effect on dye degradation activity, the MO degradation reaction constants under UV-light irradiation for SMTiO2 nanoparticles (NPs) and Au9 NCs decorated SMTiO2 photocatalysts were studied, which were 0.07 min−1 and 0.149 min−1, respectively. Hence, it takes almost half the time to completely degrade MO using Au9 NCs decorated SMTiO2 photocatalysts compared to SMTiO2 substrate. Results were analysed using the response surface methodology (RSM) to study the interaction between the reaction parameters.