Ligand fishing with immobilized enzymes offers a promising approach for screening natural active compounds in complex extracts. Key challenges in enzyme immobilization include maintaining structural integrity and enhancing loading capacity. This study employed hydrogen-bonded organic frameworks (HOFs), eco-friendly porous materials synthesized via hydrogen bonding, to immobilize elastase (ELA) through self-assembly for affinity screening of ELA inhibitors from Coreopsis tinctoria Nutt. The successful fabrication of ELA@HOF was validated using techniques such as SEM, TEM, FT-IR, XRD, XPS, TGA, and BET. HOFs significantly improved enzyme loading capacity (524.4 mg/g), immobilization rate (85.7%), specific activity (25.7 U/mg) and stability (notable acid resistance) compared to conventional methods. ELA@HOF demonstrated remarkable repeatability for ligand fishing which was reusable for 12 cycles. Seven inhibitors of ELA were extracted from extracts of C. tinctoria, which were identified by UPLC-MS combined with comparison with authentic samples as isookanin, taxifolin, marein, 7,3',5'-trihydroxyflavanone, okanin, eriodictyol, and sulfuretin. The ELA inhibitory activity and enzymatic kinetic study were further investigated, revealing a significant level of inhibition. Molecular docking technique was used to simulate the interaction between the ligand and ELA. These findings suggest the great potential of hydrogen-bonded organic frameworks for the rapid screening of active natural compounds.