A significant challenge in the treatment of low-level radioactive wastewater is the effective purification of low-concentration radionuclides. Silica-based adsorbents are advantageous for the deep-purification of low-concentration metal ions. This study investigates three primary types of silica-based adsorbents: functionalized mesoporous silica, various modified zeolites, and mesoporous calcium silicate hydrate (C-S-H). These adsorbents were synthesized and their deep-purification effects on heavy metals and radionuclides were compared. The results indicated that mesoporous silica showed relatively poor adsorption for most metal ions. Zeolites outperformed mesoporous silica, with Zn framework-modified zeolites showing enhanced adsorption for several metal ions. Notably, C-S-H displayed superior adsorption performance, achieving high adsorption capacities for various metal ions and radionuclides. Specifically, at a dose of 0.5 g/L, the adsorption efficiency of C-S-H for numerous radionuclides in nuclear power plant wastewater exceeded 92–99 %, highlighting its potential for practical applications. An in-depth analysis of the physical and chemical structure and the adsorption mechanisms of C-S-H revealed its large mesoporous structure and electrostatic attraction to cations across a wide pH range. Multivalent cations were removed through exchange with Ca2+ in C-S-H, whereas monovalent cations were removed through exchange with Na+ in C-S-H. The cyclic structure of silica-oxygen tetrahedra in C-S-H, which promotes large pore formation and provides abundant ion exchange sites, underpins its excellent adsorption properties. This study offers valuable insights for the selection and application of silica-based materials in radioactive wastewater treatment.