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A series of branched cationic β-cyclodextrin polymers (CPβCDs) with designed chemical structures were synthesized from β-cyclodextrin (β-CD), epichlorohydrin (EP) and choline chloride (CC). Indomethacin (IDM), an anionic drug, was chosen as a model drug to evaluate the drug loading capacities of CPβCDs. The formation of IDM-CPβCD complex was confirmed by 1H NMR and DSC. Phase solubility studies and Job plots indicated that CPβCDs can solubilize IDM up to 100 times of its intrinsic solubility in a 1:1 complexation form. Mechanism studies with the help of adamantane revealed that the effective complexation is a combination of inclusion complexation, charge interaction and hydrophobic interaction. In addition, IDM-CPβCDs loaded alginate hydrogels were prepared and obtained controllable release profile in dissolution tests. The tunable structures of CPβCDs make them promising drug carriers with superior drug loading capacities and controllable drug release abilities.