Due to the complexity of surgery for large-area bone injuries, implanting a large volume of materials into the injury site remains a big challenge in orthopedics. To solve this difficulty, in this study, a series of biomimetic hydroxyapatite/shape-memory composite scaffolds were designed and synthesized with programmable pore structures, based on poly(ε-caprolactone) (PCL), polytetrahydrofuran (PTMG) and the osteoconductive hydroxyapatite (HA). The obtained scaffolds presented various pore structures, high connectivity, tunable mechanical properties, and excellent shape memory performance. Moreover, the mineralization activity of the developed scaffolds could enhance the formation of hydroxyapatite and they showed good biocompatibility in vitro. The in vivo experiments show that scaffolds could promote the formation of new bone in critical size cranial defects. The programmable porous scaffold biomaterials exhibited potential application promise in bone regeneration.