A novel gas−liquid−solid circulating fluidized bed adsorber for the separation of natural products or traditional Chinese medicines from extracts was successfully developed in this work. The hydrodynamics, axial dispersion, and mixing characteristics of phases and the adsorption and desorption of Ginkgo flavonoids in macroporous resin particles with prepared extract were investigated. The results showed that with the increase of downer superficial gas velocity, the deviation degree of flow pattern from plug flow, and the liquid back-mixing in the downer were enhanced because the liquid Pe number of the downer became smaller while its axial dispersion coefficient got larger. Similar tends were found for the riser as the riser superficial gas velocity climbed. Compared with that of the downer, the flow in the riser was more close to plug flow. Investigations on the adsorption kinetics of macroporous resin particles showed that the adsorption separation of Ginkgo flavonoids from extract was controlled by the surface film mass transfer and intraparticle diffusion. Experimental results of adsorption separation of Ginkgo flavonoids in the three-phase circulating fluidized bed indicated that the air bubbles introduced in a liquid−solid circulating fluidized bed could enhance the adsorption and desorption processes, and smaller particles, lower superficial feed velocity, and adsorbate concentration were favorable for the three-phase circulating fluidized bed adsorption separation. The adsorption model of the downer and the desorption model of the riser were built, and they predicted the adsorption and desorption processes well.