Dental caries is one of the most common bacteria-related oral diseases, and the cariogenic bacteria play critical roles in its pathogenesis. Antibacterial therapy is regarded as an important approach for treating dental caries. However, the low local drug concentration and the potential generation of drug resistance limit the traditional antibacterial efficacy. Nanomaterials, such as polymeric nanoparticles and liposomes, have been widely used as functional carriers for drug delivery. The antibiotic-loaded nanomaterials have shown great potentials in enhancing the efficacy of antibacterial therapy. In addition, some functionalized nanomaterials, such as metal nanoparticles and graphene-based nanomaterials, can be used as direct antibacterial agents for physical antibacterial therapy, photothermal therapy and photodynamic therapy. Herein, we aim to provide a comprehensive understanding of dental caries and the related pathogenic bacteria, and summarize the recent progress in nanomaterials-based antibacterial treatment. Also, the antibacterial mechanisms and the concerns of nanomaterials in practical use are discussed.