Quorum sensing (QS) inhibition is recognized as a novel drug target for infections caused by drug-resistant pathogens and is an attractive strategy for the development of antipathogenic agents. Herein, we designed and synthesized three parts of3-(2-isocyanobenzyl)-1H-indole derivatives and evaluated their activity as novel quorum sensing inhibitors (QSIs). We found that 3-(2-isocyanobenzyl)-1H-indole derivatives showed promising QS inhibitory activity in the minimum inhibitory concentrations (MICs), biofilm and prodigiosin inhibition assays in Serratia marcescens. In particular, 3-(2-isocyano-6-methylbenzyl)-1H-indole(IMBI, 32) was the best candidate by biofilm and prodigiosin inhibition assays screening strategies. Further studies demonstrated, exposureIMBI (1.56 μg/mL, 1/8MICs) to S. marcescens NJ01 significantly inhibited the formation of biofilms by 42%. The IMBI treatment (1.56 μg/mL) on S. marcescens NJ01 notably enhanced the susceptibility of the formed biofilms, destroying the architecture of biofilms up to 40% as evidenced by scanning electron microscopy (SEM) and confocal laser scanning microscope (CLSM). For interference of virulence factors in S. marcescens NJ01, IMBI (3.12 μg/mL, 1/4MICs) inhibited the activity of protease, and extracellular polysaccharides (EPS)by 17% and 51% respectively, which were higher than that of the positive control vanillic acid (VAN). Furthermore, IMBI downregulated the expressions of QS- and biofilm-related genes bsmA,pigP, flhC, rssB, rsmA, and fimC by 0.13-fold to 1.46-fold. To confirm these findings, molecular docking was performed, which indicated that the binding of IMBI to SmaR, RhlI, RhlR, LasR, and CviR could antagonize the expression of QS-linked traits. In addition, molecular dynamic simulations (MD) and energy calculations indicated that the binding of receptors with IMBI was extremely stable. Most importantly, the biofilms of S. marcescens NJ01 were markedly reduced by 50% under IMBI (0.39 μg/mL, 1/32MICs)combining with 0.15 μg/mL kalamycin (KAN). In conclusion, this study highlights the potency of IMBI in inhibiting the virulence factors against S. marcescens. IMBI could be developed as an effective QS inhibitor and anti-biofilm agent to restore or improve drug sensitivity for drug-resistant pathogens.