The major cause of dental caries is attributed to Streptococcus mutans. Dental plaque which also known as oral biofilm that forms when sugar is present, S. mutans is stimulated to secrete insoluble glucans which leads to the initiation of caries lesion. Compared with synthetic antibiofilm agents, natural antibiofilm agents such as herbal plants have few adverse effects and great economic value. The purpose of this paper is to study the antimicrobial effectiveness of cinnamaldehyde, a natural plant compound, against biofilms and virulence factors of S.mutans. We have demonstrated the effects of the antimicrobial of Cinnamaldehyde on S. mutans was evaluated by measuring the MIC and MBC, growth curves, acid production, and acid tolerance. Biofilm formation by S.mutans in the presence of sub-MIC concentrations of cinnamaldehyde was measured using a crystal violet assay, and virulence-related gene expression (gtfB, gtfC, gtfD, gbpB, and LuxS) was quantified using real-time PCR. The result have shown that S. mutans was inhibited by cinnamaldehyde with a MIC of 800 µg/mL and an MBC of 1600 µg/mL, the sub-MIC concentrations of cinnamaldehyde inhibited acid production and acid tolerance. In the presence of cinnamaldehyde, genes related to biofilms and acid tolerance were also downregulated. Therefore, we hypothesis that cinnamaldehyde possesses antimicrobial properties that effectively inhibit the growth of S. mutans by targeting various key aspects of its pathogenicity, including “biofilm formation, acid production, acid tolerance, and virulence gene expression.” This study will provide the optimization of preventing and therapeutic strategies for dental caries.