To enhance osteointegration with preservation of mechanical strength, a surface modification technique using 20% surface demineralization in a controlled manner was applied to custom-built cylindrical bio-derived compact bones (20% surface-demineralized cylindrical compact bio-derived bone scaffold: SDCBS); an undemineralized version was the control. The micro-surface topography of the two types of bone scaffolds was characterized by atomic force microscopy (AFM) and scanning electron microscopy (SEM). 20% demineralization led to significant increases in surface roughness (38.19%, P=0.001) and surface area (15.1%, P=0.030), compared with the control group's, while the decrease in mechanical properties was not statistically significant. Results of orthotopic implantation for 9 months demonstrated that 20% surface demineralization caused significantly rapid and homogeneous bone remodeling at the interface compared to control and led to a significantly rapid osteointegration of SDCBS with the host bone at the early and intermediate stages of osteointegration. The study indicates the potential of SDCBS in repairing clinical bone defects, and would help direct the use of various processes of biomaterials to support defect repairs within osseous sites.