Mercapto functionalized Zr-based magnetic metal–organic framework (MUS) was synthesized and evaluated for the simultaneous removal of inorganic Sb/Se species. The adsorption kinetic study showed that the adsorption process fitted well with the pseudo-second-order kinetic adsorption model and adsorption kinetic constants were 0.188–0.591 g mg−1 min−1. Adsorption isotherm was in good agreement with the Langmuir adsorption model and the maximum adsorption capacity of Sb(V), Sb(III), Se(VI) and Se(IV) on MUS was 204, 67.6, 27.3 and 49.0 mg g−1 at 298 K. Adsorption thermodynamics showed that the adsorption process of Sb(III)/Se(IV) on MUS was spontaneous, exothermic with increased entropy, and that of Sb(V)/Se(VI) was spontaneous, endothermic with increased entropy. X-ray photoelectron spectrometer characterization showed that Zr-O clusters of MUS were essential for removing Sb(V)/Se(VI). Moreover, the combination of Zr-O clusters with mercapto may contribute to the removal of Sb(III)/Se(IV) which lead to a faster removal rate and higher adsorption capacity. The magnetic nanocomposite is promising for application in the simultaneous removal of inorganic Sb and Se species with merits of fast separation, rapid adsorption kinetics, good stability and high adsorption capacity.