In this study, an effective method was developed for the isolation and enrichment of Ginkgo biloba extract by continuous chromatography system. The adsorption and desorption ratio of flavonoids as main index, the best macroporous resin was screened out from six resins by static adsorption and desorption tests. At the same time the adsorption and desorption parameters were optimized by dynamic adsorption and desorption tests. Under optimal parameters, five operations consisting of loading, washing, desorbing, regenerating, and balancing were integrated across the continuous chromatography system for the purpose of refining 66 L of crude extract solution. The results were as follows, 198.22 g of Ginkgo biloba extracts was produced, which contained 65.83 g of flavonoids and 15.44 g of lactones. The content of flavonoids and lactones increased from 2.76 and 0.72% in the crude extract to 33.21 and 7.79%, with a recovery yield of 91.26 and 81.21%. Methodology validation showed that the proposed method had high stability and reproducibility. Compared with the traditional macroporous resin method, the proposed method had a short processing time and low solvent consumption. Our studies indicated that the newly developed method is an effective procedure for the isolation and enrichment of Ginkgo biloba extract.