Lower cellular adhesion and dense fibrous capsule formation around silicone breast implants caused by lower biocompatibility is a serious clinical problem. Preliminary work has shown that ion implantation enhances cell adhesion. Whether the biocompatibility is further enhanced by higher doses of carbon ion implantation and the mechanism by which ion implantation enhances biocompatibility remain unclear. In this study, five doses of carbon ions, which gradually increase, were implanted on the surface of silicone rubber and then the surface characteristics were surveyed. Then, cell adhesion, proliferation and migration were investigated. Furthermore, the vitronectin (VN) protein was used as a model protein to investigate whether the ion implantation affected the adsorbed protein on the surface. The obtained results indicate that enhanced cytocompatibility is dose dependent when the doses of ion implantation are less than 1 × 10 ions/cm. However, when the doses of ion implantation are more than 1 × 10 ions/cm, enhanced cytocompatibility is not significant. In addition, surface physicochemical changes by ion implantation induced a conformational change of the adsorbed vitronectin protein that enhanced cytocompatibility. Together, these results suggest that the optimum value of carbon ion implantation in silicone rubber to enhance biocompatibility is 1 × 10 ions/cm, and ion implantation regulates conformational changes of adsorbed ECM proteins, such as VN, and mediates the expression of intracellular signals that enhance the biocompatibility of silicone rubber. The results herein provide new insights into the surface modification of implant polymer materials to enhance biocompatibility. It has potentially broad applications in the biomedical field.