In this study, a new molecularly imprinted material, [email protected]2, was synthesized with glutathione (GSH) as template and mesoporous metal organic framework (UiO-66-NH2) as matrix. The molecularly imprinted polymer was modified on the surface and into the pores of the UiO-66-NH2 by surface molecular imprinting method with thin polymer layer. Based on high specific surface area (1091.93 m2 g−1) and appropriate pore size (35 nm) of the ordered mesoporous UiO-66-NH2, the adsorption capacity for GSH reached 94.43 mg g−1, and the adsorption equilibrium could be achieved within 30 min. The adsorption isotherm data of [email protected]2 could be described well by Freundlich model and the kinetic data complied well with pseudo-second-order model. In addition, the [email protected]2 showed low adsorption capacity to GSH structural analogs (QL-cys = 6.51 mg g−1), suggesting great selectivity for GSH recognition. Finally, the [email protected]2 was successfully applied for selective separation of GSH from BSA, skim milk and egg white tryptic digest.