Identification and quantification of epigoitrin (EP) in some herbs and traditional Chinese medicine (TCM) preparations are critical to pharmacokinetic study and pharmaceutical quality control due to its distinct antiviral activity. So, developing highly sensitive and selective method for detection of EP is essential for clinical treatment and drug development. In this study, a novel molecularly imprinted electrochemical sensor for detection of EP was firstly constructed. With acrylamide imprinting systems, surface imprinting on the polyaniline functionalized graphene oxide was employed to prepare molecularly imprinted polymer by electro-polymerization, which follow-up constructed afford specific binding cavities, endowing the exclusive recognition ability. Furthermore, the polyacrylamide chain is anchored to the polyaniline chain by covalent bonds, which is beneficial for raising electrochemistry signal. Under the optimized condition, the sensor demonstrates a linear wide range of 4.6×10^-7 mol/L ~ 4.6×10^-5 mol/L with a correlation coefficient of 0.9953 and a low LOD of 8.21×10^-8 mol/L (S/N = 3). Additionally, the sensor showed good stability, repeatability (RSD 1.52%) and selectivity. The method was applied to analyze EP in the extraction from Isatidis Radix with a recovery higher than 97.8% and RSD less than 1.81%. This work provided a novel strategy for on-site, real-time and rapid detection of indicator components from TCM.