In this study, a simple and effective method was proposed to improve the electrocatalytic ability of overoxidized poly(3,4-ethylenedioxythiophene)-overoxidized polypyrrole composite films modified on glassy carbon electrode for rutin and luteolin determination. The composite electrode was prepared by cyclic voltammetry copolymerization with LiClO₄-water as the supporting electrolyte. The peak current of rutin and luteolin on the composite electrode gradually decreased or even disappeared with the increase in the positive potential limit. After incubation in NaOH–ethanol solution with a volume ratio of 1:1, the composite electrodes prepared at positive potential limit greater than 1.5 V exhibited enhanced differential pulse voltammetry peak currents, reduced charge transfer resistance, larger effective specific surface area and higher electron transfer rate constant. The composite electrode prepared in the potential range of 0–1.7 V showed optimal electrocatalytic performance. The X-ray photoelectron spectroscopy results indicated that the content of –SO₂/–SO and –C=N– groups in the composite film increased significantly after incubation. Further, the Raman spectra and Fourier transform infrared spectra revealed that the thiophene ring structure changed from benzene-type to quinone-type, and the quinone-type pyrrole ring was formed. The electrocatalytic mechanism of the composite film was proposed based on the experimental results and further verified by Density Functional Theory calculation.