Much attention has been focused on the production pathway of quorum sensing (QS) signal molecule and action mode of quorum sensing inhibitor (QSI), which is also the hotspot in the field of food preservation. In this study, Shewanella baltica was the specific spoilage organism (SSO) in large yellow croaker at 4 °C storage, and SB-19 strain exhibited the highest spoilage capacity and produced the highest QS signal molecule of autoinducer-2 (AI-2) and diketopiperazines (DKPs), which was consisted of Cyclo-(L-Pro-L-Leu) and Cyclo-(L-Pro-L-Phe). After genomic sequencing and local blast, sb1370 gene was screened to be related to produce DKP in the SB-19 strain. Then knock-out strain and rescue strain of sb1370 gene were prepared, and their AI-2 and DKPs contents implied that sb1370 gene was involved in the synthesis process of DKP thorough cyclodipeptide synthase (CDPS) pathway, but did not in AI-2. Furthermore, fish fillets and mutation strains were treated by resveratrol, which strongly inhibited lipid oxidation of fillet, QS phenomenon, and sb1370 gene expression while not interfere with bacterial growth, suggesting resveratrol was an ideal QSI to inhibit DKP sb1370 gene and then QS phenomenon in S. baltica, resulting in delaying the process of fish spoilage during chilling storage.