Highly active metal-free mesoporous phosphated silica was synthesized by a two-step process and used as a SO2 hydrogenation catalyst. With the assistance of a microwave, MCM-41 was obtained within a 10 min heating process at 180 °C, then a low ratio of P precursor was incorporated into the mesoporous silica matrix by a phosphorization step, which was accomplished in oleylamine with trioctylphosphine at 350 °C for 2 h. For benchmarking, the SiO2 sample without P precursor insertion and the sample with P precursor insertion into the calcined SiO2 were also prepared. From the microstructural analysis, it was found that the presence of CTAB surfactant was important for the incorporation of active P species, thus forming a highly dispersed, ultrafine (uf) phosphate silica, (Si-P) catalyst. The above approach led to the promising catalytic performance of uf-P@meso-SiO2 in the selective hydrogenation of SO2 to H2S; the latter reaction is very important in sulfur-containing gas purification. In particular, uf-P@meso-SiO2 exhibited activity at the temperature range between 150 and 280 °C, especially SO2 conversion of 94% and H2S selectivity of 52% at 220 °C. The importance of the CTAB surfactant can be found in stabilizing the high dispersion of ultrafine P-related species (phosphates). Intrinsic characteristics of the materials were studied using XRD, FTIR, EDX, N2 adsorption/desorption, TEM, and XPS to reveal the structure of the above catalysts.