Well-ordered cubic (Pm̄3n symmetry) benzene-bridged periodic mesoporous organosilicas (PMOs) functionalized with variable contents of thiol groups were successfully synthesized via a one-step co-condensation of 1,4-bis(triethoxysilyl)benzene (BTEB) and 3-mercaptopropyltrimethoxysilane (MPTMS) in a highly acidic medium with use of cetyltrimethylammonium bromide (CTMABr) as the structure-directing agent. The materials thus obtained exhibited ordered and uniformed mesopores up to 25 mol % of MPTMS in the initial mixture. Direct evidence of the simultaneous presence of chemically attached thiol and benzene moieties was provided by solid-state 29Si and 13C NMR spectroscopy. The present cubic PMOs can be synthesized with a wide temperature window from 0 to 100 °C without any undesirable phase transformation. On the contrary, this is not possible when BTEB was replaced by tetraethoxysilane (TEOS) as the silicon source for the conventional synthesis of SBA-1 with Pm̄3n symmetry. It suggests that the benzene-linking spacer of BTEB has a beneficial effect on the enlargement of effective head group of the surfactant against the temperature changes and thus prevents phase transformation to a hexagonal mesophase. These thiol-functionalized benzene-silica materials exhibited high adsorption affinity toward metal ions such as Hg2+ and Ag+, but not for Cd2+, Co 2+, and Pb2+. Of particular interest is that the 13C NMR chemical shift of the carbon atom adjacent to the -SH group is sensitive to the Hg2+ and Ag+ ion bindings, shifting from 27 ppm to 37 and 34 ppm, respectively. Such a significant NMR shift provides clear evidence that there are strong interactions between the thiol groups and the Hg2+ and Ag+ ions.