Abstract The potential nuclear industry applications of Th make its separation from rare earth elements and U a task of great importance. Herein, materials based on phosphorodiamidate-functionalized silica were synthesized for efficient capture of Th(IV) from acidic solutions and subjected to in-depth characterization. SBA-15-O-DMAP, prepared by oxidation grafting, possessed the largest specific surface area, pore volume and grafted group density as well as abundant oxygenated groups, featuring a high Th(IV) sorption capacity, rapid sorption kinetics, and excellent selectivity. The sorption of Th(IV) by SBA-15-O-DMAP was found to be monolayer-type, chemical, endothermic, and spontaneous. In 0.01–1 M HNO3, SBA-15-O-DMAP achieved an excellent Th separation performance with separation factors of SFTh/Ln > 1,000 and SFTh/U > 50, and is thus one of the best materials reported so far for Th separation under highly acidic conditions. Theoretical calculations revealed that the high electron deficiency of the Th(IV) center compared to that of other metals contributed to the Th selectivity. In addition, SiO2 spheres functionalized with phosphorodiamidate groups allowed one to successfully separate Th(IV) from U(VI) and Ln(III) and achieve good element recoveries (>95%), a high Th decontamination factor (>4.7 × 104), and excellent reusability. Most importantly, the separation of trace Th from excess U and the extraction of Th from monazite were realized. Thus, the prepared adsorbents were concluded to be promising materials for the practical and selective isolation of Th from highly acidic solutions.