The invention relates to the technical field of electro-analytical chemistry and protein identification transducers, and discloses a synthesizing method of functionalized ionic liquid and a preparation method and application of a molecular imprinting electrochemical transducer composed of the functionalized ionic liquid, carboxylation multiwalled carbon nanotubes and glassy carbon electrodes. The preparation method of the molecular imprinting electrochemical transducer comprises the steps that the polymerizable amino-functionalized ionic liquid is used as a functional monomer, BSA is used as template protein, N, N'-methylene bisacrylamide is used as a cross-linking agent, an oxidation-reduction system composed of ammonium persulfate and TEMED is used as an initiator, after polymerization, a molecularly imprinted polymer film is formed on the surfaces of the glassy carbon electrodes decorating the carboxylation multiwalled carbon nanotubes, and then the template protein is eluted to obtain the molecular imprinting electrochemical transducer which can identify template protein in a specific mode. The molecular imprinting electrochemical transducer has the advantages of being simple in preparation, low in material cost, high in selectivity, good in biocompatibility, and capable of being used for identifying and detecting protein in aqueous solution.