The magnetic boronate based sorbents have been widely used to separation of cis-diol containing flavonoids. However, It's still challenging due to its chemical structural fragility and low grafting efficiency. The major obstacles are low concentration, the hydrophobicity of flavoniods, and complexity of crude extract solutions. For solving these problems, a new kind of covalently connect MOF@boronic acid-functionalized-COFs core–shell hybrid composites based on magnetic colloidal nanocrystal clusters (MCNCs), MCNCs@NH2-UiO-66@BTCA-BA-COFs, with high surface area, abundant binding sites and excellent chemical and structurally stability were synthesized for enhancing the structure stability and selective recognition efficiency. The alkynylation COFs were not only to be facilely grated on the surface of magnetic microsphere@NH2-UiO-66 via Schiff-based reaction but also beneficial to the further modification of azide phenylboronic acid group via click reaction. Such mentioned advantages and covalently connect click strategy could generate highly structure stable and strong binding sites for the template flavonoids (Naringin, NRG). Adsorption equilibrium experiments were reached rapidly within 120 min, and the maximum equilibrium binding capacities of MCNCs@PDA@NH2-UiO-66@BTCA-BA-COFs were 31.20 µmol g−1 for NRG. Moreover, MCNCs@PDA@NH2-UiO-66@BTCA-BA-COFs exhibited a stronger selectivity towards NRG than other competitive targets (i.e rutin, catechol, hesperetin, o-nitrophenol). The MCNCs@PDA@NH2-UiO-66@BTCA-BA-COFs have shown outstanding reusability of 91.99 % loss in enrichment performance towards NRG after seven times repeatedly. The obtained MCNCs@PDA@NH2-UiO-66@BTCA-BA-COFs-based mass spectrum (MS) methods were applied to analyze the purity of NRG products. As excepted, a commercially available NRG with purity (approximately 60 %) could be effectively extracted and concentrated to 93.15 % purity. More interestingly, the separation performance of the sorbents was influenced by hydrophilic and hydrophobic performance. This approach provided an idea for constructing a new kind of hybrid sorbents with both enhanced functionality, suitable hydrophobic performance and fast magnetic-response behavior, which is of great significance to the field of separation and purification of hydrophobic flavonoids.