The adsorption and separation of hazard metal ions, radioactive nuclides, or minor actinides from wastewater and high-level radioactive waste liquids using functional silica-based nano/micro-particles modified with various inorganic materials or organic groups, has attracted significant attention since the discovery of ordered mesoporous silica-based substrates. Focusing on inorganic and organic modified materials, the synthesis methods and sorption performances for specific ions in aqueous solutions are summarized in this review. Three modification methods for silica-based particles, the direct synthesis method, wetness impregnation method, and layer-by-layer (LBL) deposition, are usually adopted to load inorganic material onto silica-based particles, while the wetness impregnation method is currently used for the preparation of functional silica-based particles modified with organic groups. Generally, the specific synthesis method is employed based on the properties of the loading materials and the silicon-based substrate. Adsorption of specific toxic ions onto modified silica-based particles depends on the properties of the loaded material. The silicon matrix only changes the thermodynamic and mechanical properties of the material, such as the abrasive resistance, dispersibility, and radiation resistance. In this paper, inorganic loads, such as metal phosphates, molybdophosphate, titanate-based materials, and hydrotalcite, in addition to organic loads, such as 1,3-[(2,4-diethylheptylethoxy)oxy]-2,4-crown-6-Calix{4}arene (Calix {4}) arene-R14 and functional 2,6-bis-(5,6-dialkyl-1,2,4-triazin-3-yl)-pyridines(BTP) are reviewed. More specifically, we emphasize on the synthesis methods of such materials, their structures in relation to their capacities, their selectivities for trapping specific ions from either single or multi-component aqueous solutions, and the possible retention mechanisms. Potential candidates for remediation uses are selected based on their sorption capacities and distribution coefficients for target cations and the pH window for an optimum cation capture.