Bioceramic scaffolds used in bone tissue engineering suffer from a low concentration of ceramic particles (<50 wt%), because the high concentration of ceramic particles increases the brittleness of the composite. 3D printed flexible PCL/HA scaffolds with high ceramic particle concentrations (84 wt%) were successfully fabricated in this study. However, the hydrophobicity of PCL weakens the composite scaffold hydrophilicity, which may limit the osteogenic ability to some extent. Thus, as a less time-consuming, less labour intensive, and more cost-effective treatment method, alkali treatment (AT) was employed to modify the surface hydrophilicity of the PCL/HA scaffold, and its regulation of immune responses and bone regeneration were investigated in vivo and in vitro. Initially, several concentrations of NaOH (0.5, 1, 1.5, 2, 2.5, and 5 mol L-1) were employed in tests to determine the appropriate concentration for AT. Based on the comprehensive consideration of the results of mechanical experiments and hydrophilicity, 2 mol L-1 and 2.5 mol L-1 of NaOH were selected for further investigation in this study. The PCL/HA-AT-2 scaffold dramatically reduced foreign body reactions as compared to the PCL/HA and PCL/HA-AT-2.5 scaffolds, promoted macrophage polarization towards the M2 phenotype and enhanced new bone formation. The Wnt/β-catenin pathway might participate in the signal transduction underlying hydrophilic surface-modified 3D printed scaffold-regulated osteogenesis, according to the results of immunohistochemical staining. In conclusion, hydrophilic surface-modified 3D printed flexible scaffolds with high ceramic particle concentrations can regulate the immune reactions and macrophage polarization to promote bone regeneration, and the PCL/HA-AT-2 scaffold is a potential candidate for bone tissue repair.