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Recent advances in the field of nanoscience have enabled the preparation of high-surface-area supported catalysts with precise control over the individual structural components. As such, a range of factors that affect the catalytic reactivity, such as the size, shape, and composition of the nanoparticles (NPs), have been identified. Herein, high-surface-area model catalysts that were based on colloidal Pd NPs and a hexagonally ordered mesoporous carbon support were prepared and the impact of various organic capping agents for the Pd NPs on their catalytic activity towards Suzuki coupling reactions was investigated. Colloidal Pd NPs (diameter: 3 nm) were synthesized with different organic capping agents, oleylamine (OA) and trioctylphosphine (TOP), and they were subsequently incorporated into the mesopores of CMK-3 mesoporous carbon to yield OA-Pd/CMK-3 and TOP-Pd/CMK-3 nanocatalysts, respectively. The OA-Pd/CMK-3 catalyst was treated with acetic acid to generate a supported catalyst with surfactant-free Pd NPs (OA-Pd/CMK-3-A). Structural characterization revealed that the Pd NPs were uniformly dispersed throughout the mesopores of the CMK-3 support and the particle size and crystallinity of the Pd NPs were preserved following the incorporation. All of the Pd/CMK-3 nanocatalysts exhibited higher activity than commercial activated carbon supported Pd catalysts in Suzuki coupling reactions. The catalytic activities of the three Pd/CMK-3 nanocatalysts were in the following order: OA-Pd/CMK-3-A>OA-Pd/CMK-3>TOP-Pd/CMK-3. This result suggested that the presence and type of surfactants had a significant effect on the catalytic activity. The OA-Pd/CMK-3-A catalyst also showed high activity for various substrates and good recycling ability in Suzuki coupling reactions.