To explore the effects of three metabolites mixture [cyclo (leucine-proline) dipeptide, 3-phenyllactic acid and hydrocinnamic acid] produced by Lactiplantibacillus plantarum CCFM8724 on the biofilm of Streptococcus mutans and Candida albicans, and their mechanisms, dual-species biofilm formation, the production of extracellular polysaccharides and extracellular proteins, the production of quorum sensing signal molecule AI-2, and the biofilm structure were determined. The way and conformation of small moleculae metabolites binding to pathogenic targets was explored by molecular docking. The results showed that the composition significantly reduced the biofilm formation of S.mutans and C.albicans (reduction rate 79.4%), the production of water-insoluble exopolysaccharides (reduction rate 63.8%), extracellular protein (reduction rate 60.2%), and the production of quorum sensing signal molecule AI-2 (reduction rate 80.7%), and destroyed the biofilm structure at the same time. Molecular docking results revealed that the three metabolites could bind to targets such as S. mutans PtxA protein and C. albicans Fba protein, affect their sugar metabolism, and consequently inhibit biofilm formation. Through exploring the potential material basis of L. plantarum CCFM8724 to inhibit dual-species biofilm, the aim was to reveal the possible antibacterial mechanism of the composition consisting of cyclo (leucine-proline) dipeptide, 3-phenyllactic acid and hydrocinnamic acid at molecular level, and provide a theoretical basis for the development of L. plantarum CCFM8724 and its composition into oral probiotic and postbiotic products.