•A screening method using thrombin-coated magnetic beads was developed.•The method with UHPLC-Q-TOF/MS was used to screen the inhibitors from Danshen injection.•Two bound compounds were confirmed by conventional inhibitory assay.•A new inhibitor of thrombin, protocatechuic aldehyde, was reported. Thrombin was immobilized on dynabeads®M-270 epoxy by direct covalent binding method for the first time. The enzyme coated magnetic beads were combined with ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry technique to establish a simple, rapid and reliable approach for screening thrombin inhibitors from Danshen preparation. The conjugation of thrombin to the magnetic beads was characterized using scanning electron microscope, transmission electron microscope and infrared spectroscopy, and the enzyme activity was determined by the analysis of enzyme-bead ratio and peak areas of target compounds. Several factors including amount of magnetic beads, type of elution solvent, incubation temperature and time were optimized. Additionally, two thrombin-bound compounds (protocatechuic aldehyde and salvianolic acid C) in Danshen injection were validated by conventional inhibitory assay and the IC50 values were 286.11 and 66.09μg/mL, respectively. Our findings suggested that the proposed method was efficient in screening active compounds from medicinal plants.