Growth of bony tissues on titanium biomedical implants can be time-consuming, thereby prolonging recovery and hospitalization after surgery and a method to improve and expedite tissue-implant integration and healing is thus of scientific and clinical interests. In this work, nitrogen and carbon plasma immersion ion implantation (N-PIII and C-PIII) is conducted to modify Ti-6Al-4V to produce a graded surface layer composed of TiN and TiC, respectively. Both PIII processes do not significantly alter the surface hydrophilicity but increase the surface roughness and corrosion resistance. In vitro studies disclose improved cell adhesion and proliferation of MC3T3-E1 preosteoblasts and L929 fibroblasts after PIII. Micro-CT evaluation conducted 1 to 12 weeks after surgery reveals larger average bone volumes and less bone resorption on the N-PIII and C-PIII titanium alloy pins than the unimplanted one at every time point. The enhancements observed from both the in vitro and in vivo studies can be attributed to the good cytocompatibility, roughness, and corrosion resistance of the TiN and TiC structures which stimulate the response of preosteoblasts and fibroblasts and induce early bone formation. Comparing the two PIII processes, N-PIII is more effective and our results suggest a simple and practical means to improve the surface biocompatibility of medical-grade titanium alloy implants.