Background Escherichia coli (E.coli) is one of the bacteria that readily forms biofilms, posing a serious threat to food safety. Natural bioactive compounds represent an effective means to eradicate biofilm resistance, offering a novel therapeutic approach for reversing bacterial biofilm resistance. The present study aimed to clarify that paeonol could eradicate biofilm of porcine E.coli (NO. Ec032), and to explore the mechanism of paeonol eradicating Ec032 biofilm. Results The results indicated that the concentration of paeonol at 2,048 µg/mL and the intervention time at 3 hours significantly reduced the number of viable bacteria in the mature biofilm of Ec032, achieving the highest biofilm eradication rate. The total fuorescence intensity of bioflm bacteria was signifcantly decreased by 83.56%. RT-qPCR was suggested that paeonol might influence the expression of quorum sensing (QS) system and flagellum movement-related genes in biofilm bacteria, thereby reducing biofilm maturity. The Data Independent Acquisition (DIA) proteomic technique was found that paeonol could significantly decrease flagellar motility and extracellular polysaccharide content in exopoly saccharides (EPS) components, and loosen the structure of the mature biofilm. Simultaneously, paeonol could also act as a QS inhibitor (QSI) to inhibit the production of Chromobacterium violaceum 026 (CV026) violacein. In addition, molecular docking revealed that the outer membrane proteins regulator (OmpR) may be a key target of paeonol. Conclusions In summary, the research demonstrated that paeonol could act as a QSI, reducing the volume of biofilm by affecting the expression of QS and EPS matrix-related genes and proteins, thereby biofilm-eradicating of Ec032. Furthermore, this research provided a scientific basis for the development of paeonol as a novel biofilm scavenger and presented a reference for the prevention and treatment of E.coli biofilm-associated infections (BAI).