By increasing the hydrophobicity of end group, the complexation rate between α-cyclodextrin (α-CD) and poly(ethylene glycol) (PEG) derivative speeds up greatly. Based on such a huge difference of complexation kinetics, the PEG derivative with palmityloxy terminal (PEG-C16) can be successfully separated from a carboxylic acid end-functionalized analogue (PEG-COOH) by once supramolecular purification. Adding α-CD into the aqueous solution of PEG-C16/PEG-COOH mixture, PEG-C16 is encapsulated into α-CD cavity to form the crystalline inclusion complex in a very short time, while almost all of PEG-COOH molecules are still reserved in the aqueous solution. After dichloromethane extraction, the pure PEG-C16 is obtained. Moreover, the host CD can be recycled. Thus, it is an efficient green way to separate and purify the linear polymers with different terminal functionality.