The green and efficient preparation of natural products from biomass is considered an important area of interest in pharmaceutical applications. In this study, we aimed to provide a practical example with a popular traditional Chinese medicine, Anemarrhenae Rhizome, and showcase the orthogonal use of column chromatography with polyamide and macroporous adsorption resins to selectively concentrate and efficiently purify four bioactive compounds: neomangiferin (NMF), mangiferin (MF), timosaponin B-II (TS B-II), and timosaponin A-III (TS A-III). First, polyamide T60-100 was employed to fractionalize the crude extracts of Anemarrhenae Rhizome. Macroporous resin HPD400 was subsequently used to purify the xanthones and steroidal saponins. Under the optimized conditions, 2.31 g of NMF, 4.10 g of MF, 12.87 g of TS B-II, and 2.78 g of TS A-III were prepared from 1 kg of crude materials, and their purities were 90.0, 92.15, 90.8, and 92.61%, respectively. The results of this study indicate that the combined column chromatography with polyamide and macroporous adsorption resins can be referenced as a green and efficient alternative for large-scale purification of bioactive ingredients from herbal raw materials.