Polymerisation shrinkage and biofilm accumulation are the two main problems associated with dental resin composites (DRCs) that induce secondary caries, which can cause restoration failure. Polymerisation shrinkage can lead to microleakage gaps between the tooth and the DRCs, causing the aggregation of bacteria and development of secondary caries. Reducing the shrinkage stress (SS) and improving the resistance to bacterial adhesion have always been the focus of this field in modifying DRCs. A thiol-ene resin system can effectively reduce the polymerisation SS via its step-growth mechanism for delaying the gel point. Fluorinated compounds can reduce the surface free energies, thereby reducing bacterial adhesion. Thus, in this study, a range of mass fractions (0, 10, 20, 30, and 40 wt%) of a fluorinated thiol-ene resin system were added to a fluorinated dimethacrylate resin system/tricyclo decanedimethanol diacrylate to create a fluorinated methacrylate-thiol-ene ternary resin matrix. DRCs were prepared using the obtained ternary resin matrix, and their physical and chemical properties, effect on bacterial adhesion, and biocompatibility were investigated. The results demonstrated that the volumetric shrinkage and SS of the DRCs were reduced with no reduction in conversion degree even after the thiol-ene resin system was added. All DRC-based fluorinated resin systems exhibited an excellent anti-bacterial adhesion effect, as evidenced by the colony-forming unit counts, live/dead bacterial staining, and crystal violet staining tests against Streptococcus mutans (S. mutans). The genetic expressions associated with the bacterial adhesion of S. mutans were substantially affected after being cultured with fluorinated DRCs. All fluorinated DRCs demonstrated good biocompatibility through the in vitro cytotoxicity test and live/dead staining images of the L-929 cells. The above results illustrate that the DRCs based on the fluorinated methacrylate-thiol-ene resin matrix can be potentially applied in clinical practice due to their low SS and anti-bacterial adhesion effect.