Aminopropyl-functionalized silica (NH2-SiO2) was obtained via a sol-gel process using tetraethoxylsilicate (TEOS) and aminopropyltriethoxysilane (APTES). Aminopropyl group contained silica was further modified with formaldehyde to achieve a novel organic group modified silica, denoted as CH2O-SiO2. Using CH2O-SiO2 as support to prepare surported Pd catalyst (denoted as Pd/M-SiO2), small Pd nanoparticles (1-2 nm) were fabricated on CH2O-SiO2 surport. Hydrogenation of acetylene is used as probe reaction to evaluate the catalytic performance of Pd/M-SiO2. The results indicate that Pd/M-SiO2 exhibits unique catalytic property, which the selectivity of ethylene increases with the increase of acetylene conversion. In-situ DRIFTS spectra of CO adsorption show that the organic groups presented on the silica affect the electronic property of the very small Pd nanoparticles, which causes the change of reaction paths of hydrogenation of acetylene over Pd/M-SiO2 compared with traditional supported Pd catalyst.