Dental caries is a highly prevalent disease worldwide. It is caused by the cariogenic biofilms composed of multiple dynamic bacteria on dental surface. Streptococcus mutans and Streptococcus sanguinis are resident members within the biofilms and an antagonistic relationship has been shown between these two species. S. mutans, as the major causative microorganism of dental caries, has been reported to be inhibited by free D-cysteine (D-Cys). However, whether D-Cys could affect S. sanguinis and the interspecies relationship between S. mutans and S. sanguinis remains unknown. The aim of the current study was to investigate the effect of D-Cys on the growth and cariogenicity of dual-species biofilms formed by S. mutans and S. sanguinis. We measured dual-species biofilms biomass, metabolic activity, lactate production. We also detected the biofilms structure, the ratio of live/dead bacteria, extracellular polysaccharide (EPS) synthesis and bacterial composition in the dual-species biofilms. We found that D-Cys could reduce the metabolic activity and lactic acid production of dual-species biofilms (p < 0.05). In addition, biofilms formation, the proportion of S. mutans in dual-species biofilms, and EPS synthesis were decreased with D-Cys treatment. The results suggested that D-Cys could inhibit the growth and cariogenic virulence of dual-species biofilms formed by S. mutans and S. sanguinis, indicating the potential of D-Cys in clinical application for caries prevention and treatment.