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This study is the first report on the synthesis, characterization and application of amine-functionalized mesoporous nanocomposites based on natural rubber (NR) and wormhole-like mesostructured silica (WMS). In comparison with amine-functionalized WMS (WMS-NH₂), a series of NR/WMS-NH₂ composites were synthesized via an in situ sol-gel method in which the organo-amine group was grafted onto the nanocomposite surface via co-condensation with 3-aminopropyltrimethoxysilane (APS) as the amine-functional group precursor. The NR/WMS-NH₂ materials had a high specific surface area (115–492 m² g⁻¹) and total pore volume (0.14–1.34 cm³ g⁻¹) with uniform wormhole-like mesoporous frameworks. The amine concentration of NR/WMS-NH₂ (0.43–1.84 mmol g⁻¹) was increased with an increase in the APS concentration, corresponding to high levels of functionalization with the amine groups of 53–84%. The H₂O adsorption–desorption measurement revealed that NR/WMS-NH₂ possessed higher hydrophobicity than WMS-NH₂. The removal of clofibric acid (CFA), a xenobiotic metabolite of the lipid-lowering drug clofibrate, from the aqueous solution using WMS-NH₂ and NR/WMS-NH₂ materials was investigated using a batch adsorption experiment. The adsorption was a chemical process in which the pseudo-second order kinetic model expressed the sorption kinetic data better than the pseudo first-order and Ritchie-second kinetic order model. In addition, the CFA adsorption sorption equilibrium data of the NR/WMS-NH₂ materials were fitted to the Langmuir isotherm model. The NR/WMS-NH₂ with 5% amine loading had the highest CFA adsorption capacity (6.29 mg g⁻¹).