Repair and regeneration of large bone defects is still a challenge, especially for defects which are the irregular and complex. Three-dimension (3D) printing, as an advanced fabrication technology, has been received considerable attentions due to its high precision, customized geometry and personalization. In this study, 3D porous polylactic acid/nano hydroxyapatite (PLA/nHA) composite scaffolds with enhanced osteogenesis and osteoconductivity were successfully fabricated by desktop fused deposition modeling technology. Morphological, composition and structural analysis revealed that nHA was successfully introduced into the PLA system and homogeneously dispersed in the printed PLA/nHA scaffolds. In vitro antibacterial experiment confirmed that the printed porous PLA/nHA scaffolds have good ability for loading and releasing vancomycin and levofloxacin. Meanwhile, MG-63 cells were used to evaluate the cytocompatibility of printed porous PLA/nHA scaffolds by proliferation and cellular morphological analysis. In addition, rabbit model was established to evaluate the osteogenesis and osteoconductivity of printed PLA/nHA scaffolds. All these results suggested that the 3D printed PLA/nHA scaffolds have great potential for repairing and regeneration of large bone defects.