A simple yet efficient strategy is urgently desired to prepare smart metal-organic framework nanocomposite for highly selective capture and separation of natural flavone from complex extraction samples. In this study, novel hydrophilic magnetic borate-functionalized metal-organic framework nanocomposites (Fe3O4@PDA@BA-MOFs) were designed and synthesized for selective enrichment of cis-diol containing luteolin (LTL). The well-known solvothermal reaction was adopted to prepare the magnetic core Fe3O4, followed by self-polymerization of dopamine, to create the polydopamine (PDA) onto Fe3O4. Thanks to the hydroxyl and amino groups of PDA, Zn2+ was easily adhered to the surface, taking advantage of magnetic response to fabricate the Fe3O4@PDA@ BA-MOFs by layer-by-layer assembly strategy with borate ligand (5-boronobenzene-1,3-dicarboxylic acid). The ultrahigh surface area, uniform morphology, high saturation magnetization, excellent hydrophilicity and strong magnetic responsiveness of the as-prerared smart porous adsorbent (i.e. Fe3O4@PDA@BA-MOFs) were highly confirmed by the characterizations. Based on the batch mode experiments, Fe3O4@PDA@BA-MOFs showed high selectivity, obvious binding kinetics, large adsorption capacity, and excellent reusability (above 91.23% at least six repeated adsorption-desorption cycles). Moreover, pH-responsive capture and release mechanism based on the boronic acid affinity was proved, and Fe3O4@PDA@BA-MOFs would be good candidates for the enrichment and purification of the LTL.