Background: Biodegradable polymeric scaffolds are critical to repair a large bone defect, which can provide a porous and network microenvironment for cell attachment and bone tissue regeneration. A multifunctional biodegradable PCL/HA composite was prepared with the blending of poly(ε-caprolactone) (PCL) and hydroxyapatite nanoparticles (HA). Subsequently, the PCL/HA scaffolds implants were produced by the screw extrusion/melting deposition forming method using PCL/HA composite as a raw material in this work. Results: Through a serial of in vitro assessments, it is found that the PCL/HA composite possesses good biodegradability, good biocompatibility, and steady drug release performance, which can improve the cell proliferation of osteoblast cells MC3T3-E1. Meanwhile, in vivo experiments were carried out for the rats with skull defect and rabbits with bone defects. It is observed that the PCL/HA scaffolds implants allow the adhesion and penetration of bone cells, which enables the growth of bone cells and bone tissue regeneration. With a composite design to load an anticancer drug and achieve sustained drug release, the scaffolds could enhance bone repair and be expected to inhibit the tumor cells and improve patient outcomes. Conclusions: This work signifies that PCL/HA composite can be used as the potential biodegradable scaffolds for bone repairing after bone malignant tumor resection.