Designing new chelating sorbents for the sorption of thorium as (Th4+) has become an impending challenge. This study describes a simple one-pot in situ co-precipitation method was used to synthesize a multifunctional magnetic-chitosan nanocomposite core-shell for enhanced Th4+ ions sorption from aqueous solutions. The synthesized biosorbent was well characterized by various techniques such as FTIR, XRD, pHzpc, TEM, VSM and elemental analysis. The sorption behavior of magnetic-chitosan nanocomposite (R-I) is systematically compared to the performance of functionalized magnetic-chitosan nanocomposite (R-II). The magnetic nanocomposites sizes around 25.0 nm. The grafting of methylene phosphonic groups on chitosan increased Th4+ sorption efficiency. Maximum sorption capacities reach 89.7 and 142.3 mg Th g−1 for R-I, and R-II sorbents, respectively at pH 3.5. Kinetics, isotherms, and thermodynamic behaviors of Th4+ ions sorption into the synthesized nanocomposite from an aqueous solution were studied in detail. The studies showed that the Langmuir isotherm and pseudo-second order model gave a better description for the sorption process. The sorption is spontaneous, endothermic and controlled by entropic change. EDTA solutions (0.25 M) can be efficiently used for metal recovery and sorbent can be recycled for at least 5 cycles without significant loss in sorption/desorption performances.