A new mini‐deposition system (MDS) was developed to fabricate scaffolds with interconnected pore structures and anatomical geometry for bone tissue engineering. Polycaprolactone/hydroxyapatite (PCL/HA) composites with varying hydroxyapatite (HA) content were adopted to manufacture scaffolds by using MDS with a porosity of 54.6%, a pore size of 716 μm in the x‐y plane, and 116 μm in the z direction. The water uptake ratio and compressive modulus of PCL/HA composite scaffold increase from 8 to 39% and from 26.5 to 49.8 MPa, respectively, as the HA content increases from 0 to 40%. PCL/HA composite scaffolds have better wettability and mechanical properties than pure PCL scaffold. A PCL/HA composite scaffold for mandible bone repair was successfully fabricated with both interconnected pore structures and anatomical shape to demonstrate the versatility of MDS. POLYM. ENG. SCI., 2012. © 2012 Society of Plastics Engineers