The invention discloses a method for preparing a poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) composite modified electrode. The method comprises the following steps of: uniformly mixing PEDOT:PSS aqueous dispersion liquid and Nafion, which are taken as raw materials, and then directly dispensing a mixture on the surface of a composite modified electrode; and in the conventional three-electrode system, performing secondary electrochemical doping by using hydrophobic ionic liquid, and thus obtaining the PEDOT:PSS composite modified electrode which is high in water resistance and high in conductivity. The PEDOT:PSS composite modified electrode which is prepared by the method fully combines the film-forming property of the PEDOT:PSS aqueous dispersion liquid, the adhesion characteristic, biological compatibility and anti-interference characteristic of the Nafion, high conductivity and hydrophobicity of the ionic liquid and the electrochemical catalysis characteristic of a nanometer material, can be applied to electrochemical biosensors or electrochemical sensors, is directly applicable to electrochemical detection of auxin, roxithromycin, vitamin C, benzenediol isomer, organophosphorus, glucose, hydrogen peroxide and the like, and has the characteristics of good detection effect, short response time, high water resistance, wide linear range, high sensitivity, high anti-interference, high stability and the like.