The present research aims to develop a Ca-Zn ion-incorporated surface functionalized 3D Ti cancellous bone scaffold for bone defect repair. The scaffold is designed to mimic human cancellous bone architecture through selective laser melting-based additive manufacturing. The chemical-based surface modification approach employed here created a Ca and Zn ions incorporated nano-porous surface layer with enhanced surface roughness and hydrophilicity. The modified biomimetic scaffold improved corrosion resistance behaviour with ICORR and ECORR values of 0.174 and 0.0097 respectively. It is learned that incorporating Zn as ZnO over the scaffold has antibacterial activity against Staphylococcus aureus and Escherichia coli. The cellular response of MG-63 to the modified scaffold was evaluated through in-vitro studies which focus on the cytocompatible properties. The intra-osseous biomimetic Ti-Na-Ca:Zn 3D scaffold revealed significant improvement in the osseointegration capabilities in terms of bone mineral density (BMD) and bone volume/total volume (BV/TV) in the rabbit model. The osseointegration potential at the Ti-Na-Ca:Zn interface was evidenced by histological analysis and micro-CT imaging. In addition to this, the remarkable upregulation of osteogenic genes such as OCN, COL1A1, OPN, ALP, RUNX2, and OSX evidences the dynamics of the osseointegration process at each surgical period. This Ca and Zn surface functionalised porous architecture of the 3D Ti cancellous bone scaffold similar to bone with enhanced biological response and bone integration can potentially allow implant customisation by utilizing additive manufacturing technology with improved clinical outcomes.