In this study, the mechanism of quorum sensing inhibition (QSI) by plant-oriented organic molecules, vanillin, was investigated. During the biofouling experiment with Pseudomonas aeruginosa as a model bacterium in the forward osmosis (FO) membrane process, the addition of 1 mM vanillin showed remarkable mitigation of biofouling without both bactericidal and bacteriostatic effects. Subsequently, bioassay of quorum sensing (QS) molecules and RNA sequencing of P. aeruginosa were conducted to figure out QSI mechanism. Interestingly, the bioassay result showed that the addition of 1 mM vanillin as the QSI was not sufficient to degrade the QS signal molecules such as N-Hexanoyl-DL-homoserine lactone. On the other hands, the analysis of RNA gene expressions exhibited that the significant down-regulation of QS receptors while there was not any noticeable changes in gene expressions related to synthesis of QS signal molecules. The down-regulation of QS receptor genes suppressed the hierarchical and interconnected QS system of P. aeruginosa, thus contributed as the main mechanism of QSI. The result of this study implies the potential applicability of QSI by plant-oriented organic molecules to mitigate biofouling in membrane processes where the concentration of organic matters is not important.