In this research, the authors studied the synthesis of a silicon-based quaternary ammonium material based on the coupling agent chloromethyl trimethoxysilane (KH-150) as well as its adsorption and separation properties for Th(IV). Using FTIR and NMR methods, the silicon-based materials before and after grafting were characterized to determine the spatial structure of functional groups in the silicon-based quaternary ammonium material SG-CTSQ. Based on this, the functional group grafting amount (0.537 mmol·g−1) and quaternization rate (83.6%) of the material were accurately calculated using TGA weight loss and XPS. In the adsorption experiment, the four materials with different grafting amounts showed different degrees of variation in their adsorption of Th(IV) with changes in HNO3 concentration and NO3− concentration but all exhibited a tendency toward anion exchange. The thermodynamic and kinetic experimental results demonstrated that materials with low grafting amounts (SG-CTSQ1 and SG-CTSQ2) tended to physical adsorption of Th(IV), while the other two tended toward chemical adsorption. The adsorption mechanism experiment further proved that the functional groups achieve the adsorption of Th(IV) through an anion-exchange reaction. Chromatographic column separation experiments showed that SG-CTSQ has a good performance in U-Th separation, with a decontamination factor for uranium in Th(IV) of up to 385.1, and a uranium removal rate that can reach 99.75%.