In order to screen more efficient， non-toxic and green inhibitors of Vibrio parahaemolyticus， molecular docking was applied to screen natural small molecules with potential antimicrobial activity using the outer membrane protein OmpW of V. parahaemolyticus as receptor. Then citric acid and caffeic acid which had ideal docking results were used for further experimental verification. On the basis of determining the minimal inhibitory concentrations （MIC）， the changes of sensitivity to small molecules and the killing curves of V. parahaemolyticus with outer membrane removed and cell wall removed were studied， and whether outer membrane protein OmpW was the binding site of citric acid and caffeic acid was analyzed to verify the correctness of the method based on molecular docking for screening bacterial inhibitors. The results showed that the MICs of citric acid and caffeic acid on V. parahaemolyticus ATCC17802 were both 2 mg/mL. Compared with the control， the MICs of the cells with outer membrane removed and cell wall removed were reduced by 16 to 64 times， which indicated that citric acid and caffeic acid were likely to act on outer membrane protein OmpW of V. parahaemolyticus， and molecular docking results also indicated that these two small molecules formed non-covalent binding with OmpW to fulfill inhibition. Validation tests showed that these two small molecules also restrained other strains of V. parahaemolyticus. Conclusion： citric acid and caffeic acid are effective inhibitors of V. parahaemolyticus （MIC < 5 mg/mL）， and their action site is likely to be the outer membrane protein OmpW. The use of molecular docking to search for efficient and green bacterial inhibitors has a broad development prospect.