In this study, a ligand fishing method for the screening of α‐glucosidase inhibitors from Ginkgo biloba leaf was established for the first time using α‐glucosidase immobilized on the magnetic metal‐organic framework. The immobilized α‐glucosidase exhibited enhanced resistance to temperature and pH, as well as good thermal stability and reusability. Two ligands, namely quercitrin and quercetin, were screened from Ginkgo biloba leaf and identified by ultra‐high performance liquid chromatography‐tandem mass spectrometry. The half‐maximal inhibitory concentration values for quercitrin and quercetin were determined to be 105.69 ± 0.39 and 83.49 ± 0.79 µM, respectively. Molecular docking further confirmed the strong inhibitory effect of these two ligands. The proposed approach in this study demonstrates exceptional efficiency in the screening of α‐glucosidase inhibitors from complex natural medicinal plants, thus exhibiting significant potential for the discovery of antidiabetic compounds.