Abstract The synthesis of mesoporous organosilicas (MOs) using co-condensation for a high ratio of a long and flexible chained organosiloxane bridge with silica precursor (e.g. tetraethylorthosilicate (TEOS)) is a complex and challenging task. By complementing the experimental characterisations with density functional calculations, The critical ratio of the urea-based organosiloxane bridge (BTPU) to tetraethyl orthosilicate of 1:8 was identified to delivers reliably stable urea bridged MO (MO-urea) with relatively large surface area and mesoporosity. Moreover, the Pd nanoparticles supported on the pore channels of MO-urea achieve a narrow distribution size averaging at a diameter of ~2 nm. This fine distribution is driven by the Pd nanoparticles nucleating only on the exposed SiO2 section of MO-urea while the BTPU bridges punctuate the growth of the Pd nanoparticles limiting their size. As a result, the obtained Pd@MO-urea exhibits excellent multifunctional catalytic activity for hydrogen production from formic acid and p-nitrophenol (PN) reduction in aqueous media with four folds increase in yield compared to the non-punctuated Pd nanoparticles.