Large amounts of solid medium containing cordycepin, used in the industrial production of Cordyceps militaris through solid fermentation, are discarded as waste and contaminate the environment. We have developed a new column chromatographic extraction (CCE) method for the extraction of cordycepin from this waste and a preparation method for further separation and purification. Dried waste material was imbibed in four times its volume of water for 6h, transferred to columns and eluted with water. Eluates were directly separated with macroporous resin DM130 columns followed by purification steps, including precipitation, crystallization, and polyamide column chromatography. Extraction rates of more than 97% were obtained with 12 volumes of water for a single column and 4 volumes of water for eluates circulated through 3 different columns designed to concentrate cordycepin. Cordycepin (98% pure) was obtained following the separation and purification processes, with an overall recovery rate of more than 90%. The CCE method has high extraction efficiency, uses a minimum volume of solvent and can be used for both quantitative analysis and large preparations of cordycepin from waste. The preparation method is simple, highly efficient, energy-saving, environmentally friendly, and has been demonstrated to be effective for large preparations of cordycepin from waste with low equipment and operating costs.