Abstract A receptor affinity chromatographic selection method was developed for screening the bioactive compounds binding to β 2-adrenoceptor ( β 2-AR) in Coptidis rhizome. The bioactive compounds were analyzed by molecular recognition with a β 2-AR affinity column. The retention compounds eluted from the β 2-AR column were separated online with reverse-phase high-performance liquid chromatography by column switching technology, and identified by a coupled ion-trap mass spectrometer. Four compounds were screened as the bioactive compounds of Coptidis rhizome and identified as 2,9,10-trimethoxy-3-hydroxyl-protoberberine (jateorhizine), 2,3-methylenedioxy-9-methoxy-protoberberine, 2,3,9,10-tetramethoxy-protoberberine (palmatine) and 2,3-methylenedioxy-9,10-dimethoxy-protoberberine (berberine). The association constants of jatrorrhizine, palmatine and berberine to the β 2-AR were determined by the zonal elution method with standards. Berberine and palmatine had only one type of binding site on the immobilized β 2-AR. Their association constants were (2.28 ± 0.11) × 10 4/M and (3.00 ± 0.10) × 10 4/M, respectively. Jatrorrhizine had at least two type of binding sites on the immobilized β 2-AR, and the corresponding association constants were (2.20 ± 0.09) × 10 −4/M and (6.78 ± 0.001) × 10 5/M.