The invention discloses a method for preparing functionalized acidic ionic liquid with fluorous biphasic property, comprising the following steps: firstly adding polyethylene glycol (PEG) into toluene to undergo azeotropic distillation at reduced pressure to remove water; under the condition of ice bath, dropwise adding thionyl chloride into mixed liquor of acid binding agents, solvents and PEG, and carrying out the reaction at normal temperature; washing the product with diethyl ether and washing the product with PEG below 1000 with acid water to obtain the PEG product with two terminals chlorinated; then reacting sodium ethylate or sodium hydride with imidazole to prepare imidazole sodium and stirring the imidazole sodium; then taking ethanol as the solvent and stirring the imidazole sodium and the PEG product with two terminals chlorinated; after pump filtration, carrying out rinsing to remove the impurities and extracting aqueous phase with dichloromethane; then taking ethanol as the solvent and dropwise adding cycloparaffin sultone into the product obtained in the previous step and stirring the mixture; taking ethanol as the solvent and dropwise adding acid into the product obtained in the previous step and stirring the mixture; and finally washing the product with diethyl ether, toluene or petroleum ether, thus obtaining the required product. The preparation method is simple to operate and high in yield rate.