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Natural products often contain a large number of structurally similar compounds, however, from which the isolation of monomer compounds is complex and time-consuming. In this study, for the first time, a Zr-based metal-organic framework (MOF), UiO-66, was used for the separation of three isoflavones (genistein (GEN), puerarin (PUE), and daidzein (DDZ)) with similar structures. UiO-66 was demonstrated to have a distinct high adsorption capacity (q e , 105.42 ± 2.36 mg/g) for GEN with high separation factors from PUE (α, 35.52 ± 1.22) and DDZ (α, 7.41 ± 0.76), dramatically increasing the purity of GEN from ∼33–92% after primary separation. According to SEM-EDS and XPS characterizations together with RDF analysis, GEN and PUE were adsorbed on the surface of UiO-66 at the same dominant Zr cluster site (O...Zr), while DDZ was bound onto the inferior site via weak hydrogen bonding (H...O), indicating the separation of GEN from PUE was in a competitive manner, while the separation from DDZ was selective. For these three drugs, their adsorption kinetics and adsorption isotherms conformed Pseudo-second-order kinetic model and Langmuir model, respectively, indicating that the monolayer adsorption of isoflavones on UiO-66 surface was the dominant mechanism. The thermodynamic study demonstrated that both adsorptions of GEN and PUE were spontaneous (Δ G 0 < 0), whereas the DDZ adsorption is non-spontaneous (Δ G 0 > 0). Compared to traditional separation techniques, this study provided a simple and efficient approach to isolate structurally similar compounds from natural products in drug discovery. [Display omitted] • UiO-66 can effectively separate GEN from three structurally similar isoflavones(GEN, PUE, and DDZ). • The adsorption of GEN and PUE on UiO-66 was spontaneous, whereas that of DDZ was non-spontaneous. • GEN was separated from PUE and DDZ in a competitive and selective manner, respectively. • MOF adsorption is a promising approach for effectively separating similar structural natural compounds. [ABSTRACT FROM AUTHOR]