Poor mechanical properties and bacterial infection are the main problems faced by dental restorative resins in clinical use. In this study, graphene quantum dots (GQDs) grafted with imidazole groups and mesoporous silica (MSN) are co-filled in a dental resin to impart excellent antimicrobial activity and mechanical properties to the dental resin. The higher specific surface area of GQDs and MSN results in an increased contact area with the resin matrix, which enhances the strength of the dental composite resin. The introduction of GQDs significantly improves the antimicrobial activity of the resin. The inhibition efficiency of the composite resin against Streptococcus mutans reached 99.9% with the addition of GQDs at only 0.2 wt.%. When MSN and GQDs are co-filled, MSN interferes with the release of GQDs, thus reducing the antimicrobial activity of the dental resin but improving the cyto-compatibility. By reasonably adjusting the amount of GQDs and MSN, the dental composite resin can exhibit excellent antimicrobial properties, mechanical properties and cyto-compatibility at the same time.