In the present study, the 3D printer method for fabricating porous bone scaffolds with Polylactic Acid (PLA) printed was used by Fused Deposition Modelling (FDM). Then, the prepared 3D scaffold coated with alginate composed with various amounts of Hydroxyapatite (HA) using the freeze-drying technique. After the fabrication of novel functional graded materials scaffold, the mechanical strength and biological behavior were investigated. The Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD) analysis used to characterize the morphology and phase characterization. The structure of the porous scaffold was simulated using the ABAQUS analysis method and their mechanical and physical properties were extracted. Also, strong antibacterial properties were observed for all samples with increasing HA nanoparticles against gram-positive and gram-negative bacterial suspensions. These bio-nano composites are compatible with the pH of the blood. In general, it was found that the most suitable bio-nano composite is the sample with 10 wt % HA nanoparticles. The elastic modulus increased from 350 MPa to 394 MPa with the addition of HA nanoparticles, while the porosity percentages decreased from 44 % to 36 %. The compressive strength increases from 25.2 MPa to 32.7 MPa with the addition of 30 wt% HA nanoparticles. The obtained results showed that the bio-nano composites prepared in this study were suitable for further development in bone substitutes with desirable mechanical properties. The alginate/HA material properties reported from the numerical approach, have an acceptable agreement with experimental results. Furthermore, the numerical study indicated that the scaffold compressive strength increases from 22.8 MPa (S1) to 31.2 MPa (S4) with the addition of 30 wt % HA nanoparticles. Nanoindentation test explains that the indenter penetration decreases from 82.163 nm to 69.338 nm with the addition of 30 wt% HA nanoparticles. As a consequence, PLA-alginate/20 wt % HA (S3) and, PLA-alginate/30 wt% HA (S4) have the best mechanical properties. Although due to lower biological advantages of S4 concerning S3, PLA-alginate/20 wt % HA (S3) chose as an appropriate bio-nanocomposite for orthopedic application.