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Chlorogenic acid (CGA) is a polyphenol compound with health functions. In order to enrich and purify CGA from mulberry leaf extracts efficiently, three-dimensional porous cellulose-based microspheres modified with ionic liquid functional groups (CMs-ILs) was developed. In terms of adsorption properties, compared with three different commercial macroporous resins (D101, NKA-9, and AB-8), CMs-ILs exhibited a greater adsorption capacity (103.6 mg/g) and a faster adsorption rate to reach equilibrium (40 min). The density functional theory (DFT) calculations were implemented to study the adsorption mechanism. It was showed that hydrogen bonding and π-π stacking were the main interactions between CGA and ILs. The results of a contact angle test and water drop diffusion experiments indicated that the super hydrophilic surface and porous structures of CMs-ILs accelerating the mass transfer rate, leading to a fast adsorption rate. Moreover, the relative adsorption capacity was still over 85% of the original after reusing for 5 times. Therefore, CMs-ILs would be a promising material for enrichment of CGA from natural plants.