Thiol-functionalized mesoporous silica and materials potentially dedicated to diverse applications of composite materials, metal colloids, and metal catalysts, etc. Here, we developed a new synthesis route for 3-methacryloxypropyl trimethoxy silane (MPTMS) functionalized mesoporous silica (KIT-6), achieving a 71.5 % enhancement in thiol functionalization on KIT-6 surfaces. Characterization using XRD, TEM, BET, FTIR, Raman, 29Si NMR, XPS, and ICP-OES revealed structural and morphological features. XRD, TEM, and BET confirmed the three-dimensional structural stabilization of mesoporous silica with ~4 nm pore diameter and a surface area of 1451 m2 g-1. FTIR, Raman, and 29Si NMR studies established the mechanism of thiol functionalization, the formation of a new wormhole chain structural framework (WCSF), and stabilization through hydrogen bonding within the mesopores. The 29Si NMR spectra showed characteristic peaks (T3, T2, Q4, Q3) indicating self-condensed functionalized thiols with siloxane networks. XPS analysis validated enhanced thiol functionalization, indicating a structurally homogeneous WCSF suitable for mercury adsorption. ICP-OES measured a mercury adsorption capacity of 3199.6 mg g-1 for KIT-6, with an Hg2+/S ratio of 1.8, corroborated by molecular structure and mechanism analysis. This innovative thiol functionalization approach enhances the efficacy of applications such as extracting Hg2+ from contaminated sources.