The potential industrial application of thorium (Th), as well as the environmental and human healthy problems caused by thorium, promotes the development of reliable methods for the separation and removal of Th(IV) from environmental and geological samples. Herein, the phosphonate-amino bifunctionalized mesoporous silica (PAMS) was fabricated by a one-step self-assembly approach for enhancing Th(IV) uptake from aqueous solution. The synthesized sorbent was found to possess ordered mesoporous structures with uniform pore diameter and large surface area, characterized by SEM, XRD, and N2 sorption/desorption measurements. The enhancement of Th(IV) uptake by PAMS was achieved by coupling of an access mechanism to a complexation mechanism, and the sorption can be optimized by adjusting the coverage of the functional groups in the PAMS sorbent. The systemic study on Th(IV) sorption/desorption by using one coverage of PAMS (PAMS12) shows that the Th(IV) sorption by PAMS is fast with equilibrium time of less than 1 h, and the sorption capacity is more than 160 mg/g at a relatively low pH. The sorption isotherm has been successfully modeled by the Langmuir isotherm and D-R isotherm, which reveals a monolayer homogeneous chemisorption of Th(IV) in PAMS. The Th(IV) sorption by PAMS is pH dependent but ionic strength independent. In addition, the sorbed Th(IV) can be completely desorbed using 0.2 mol/L or more concentrated nitric acid solution. The sorption test performed in the solution containing a range of competing metal ions suggests that the PAMS sorbent has a desirable selectivity for Th(IV) ions.