Hedyotis diffusa is known for its significant medical value, such as curing pneumonia in children, remedying gastritis, and relieving gynecological inflammation. In this study, a new assay based on ultrafiltration–liquid chromatography was developed for the rapid screening and identifying of ligands for α-glucosidase inhibitors from Hedyotis diffusa. Eleven potential α-glucosidase inhibitors were found in the crude extract, and four of these were separated successfully by high-speed countercurrent chromatography: 2-hydroxyl-3-methyl anthraquinone, 2-methyl-3-hydroxyl anthraquinone, 2-hydroxyl-3-methyl-1-methoxyl anthraquinone, and a novel compound. The percent purities of the compounds are 97.71, 95.96, 87.60, and 93.66%, respectively. Results of our study demonstrated that our systematic screening, identification, and isolation of bioactive components in Hedyotis diffusa using ultrafiltration–liquid chromatography–diode array detector, liquid chromatography–electrospray ionization–tandem mass spectrometry, and high-speed countercurrent chromatography are feasible and efficient. Our approach also can be used to rapidly screen and separate other enzyme inhibitors.