The use of deep eutectic solvents (DESs) to extract natural products has attracted considerable attention in recent years. However, the recovery of extracted compounds and DES from DES extracts is still a barrier, which restricts the large-scale application of DESs. Here, we proposed a high-speed countercurrent chromatography (HSCCC)-based method to recover extracted compounds and DES. As a proof of concept, the chrysanthemum DES extract was selected to verify the method. We first prepared a series of DES-based solvent systems and screened them based on their physical and chemical properties. Only the system composed of choline chloride/l-malic acid, water, and ethyl acetate (1:1:1, v/v/v) was suitable. By using the solvent system for HSCCC separation, the target compounds and DES in the chrysanthemum DES extract were both successfully recovered with high recovery yields over 95%. Then, we investigated the reusability of the recovered DES and found that it could be repeatedly reused for three times without any performance deterioration. All these results indicated that the proposed method is feasible and efficient, which has great potential for application. Moreover, the method may also be used in other fields where the separation process is needed, such as organic synthesis, chemical separation, bioseparation, and biotransformation.