Cortex Morin Radicis (CMR) is the dried root bark of Morus alba. L. It has a variety of effects such as antibacterial, anti-tumour, treatment of cardiovascular diseases or upper respiratory tract disease and so on. The pursuit for drugs selected from Cortex Mori Radicis having improved therapeutic efficacy necessitates increasing research on new assays for screening bioactive compounds with multi-targets. In this work, we applied immobilized β1-AR and β2-AR as the stationary phase in chromatographic column to screen bioactive compounds from Cortex Morin Radicis. Specific ligands of the two receptors (e.g. esmolol, metoprolol, atenolol, salbutamol, methoxyphenamine, tulobuterol and clorprenaline) were utilized to characterize the specificity and bioactivity of the columns. We used high performance affinity chromatography coupled with ESI-MS to screen targeted compounds of Cortex Morin Radicis. By zonal elution, we identified morin as a bioactive compound simultaneously binding to β1-AR and β2-AR. The compound exhibited the association constants of 3.10 × 104 and 2.60 × 104 M-1 on the β1-AR and β2-AR column. On these sites, the dissociation rate constants were calculated to be 0.131 and 0.097 s-1. Molecular docking indicated that the binding of morin to the two receptors occurred on Asp200, Asp121, and Val122 of β1-AR, Asn312, Thr110, Asp113, Tyr316, Gly90, Phe193, Ile309, and Trp109 of β2-AR. Likewise, mulberroside C was identified as the bioactive compound binding to β2-AR. The association constants and dissociation rate constants were calculated to be 1.08 × 104 M-1 and 0.900 s-1. Molecular docking also indicated that mulberroside C could bind to β2-AR receptor on its agonist site. Taking together, we demonstrated that the chromatographic strategy to identify bioactive natural products based on the β1-AR and β2-AR immobilization, has potential for screening bioactive compounds with multi-targets from complex matrices including traditional Chinese medicines.