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Three-dimensional (3D) printing techniques have received considerable focus in the area of bone engineering due to its precise control in the fabrication of complex structures with customizable shapes, internal and external architectures, mechanical strength, and bioactivity. In this study, we design a new composition biomaterial consisting of polylactic acid (PLA), and halloysite nanotubes (HNTs) loaded with zinc nanoparticles (PLA+H+Zn). The hydrophobic surface of the 3D printed scaffold was coated with two layers of fetal bovine serum (FBS) on the sides and one layer of NaOH in the middle. Additionally, a layer of gentamicin was coated on the outermost layer against bacterial infection. Scaffolds were cultured in standard cell culture medium without the addition of osteogenic medium. This surface modification strategy improved material hydrophilicity and enhanced cell adhesion. Pre-osteoblasts cultured on these scaffolds differentiated into osteoblasts and proceeded to produce a type I collagen matrix and subsequent calcium deposition. The 3D printed scaffolds formed from this composition possessed high mechanical strength and showed an osteoinductive potential. Furthermore, the external coating of antibiotics not only preserved the previous osteogenic properties of the 3D scaffold but also significantly reduced bacterial growth. Our surface modification model enabled the fabrication of a material surface that was hydrophilic and antibacterial, simultaneously, with an osteogenic property. The designed PLA+H+Zn may be a viable candidate for the fabrication of customized bone implants.