It is significant to endow the bone tissue scaffolds with the elasticity and capacity of establishing a bone remodelling microenvironment, and thus to exploit the endogenous regeneration functions of bone to regenerate the critical-sized bone defects. To this end, this work constructed the calcium sulphate (CaSL)-loaded silk fibroin (SF)/gelatin elastic hydrogel scaffolds by means of an indirect three-dimensional (3D) printing technique. The results showed that the indirect 3D printing technique was a general method to prepare the elastic SF-based composite hydrogel scaffolds. In vitro experiments demonstrated that the as-prepared scaffolds could establish an acidic and high calcium ion concentration of microenvironment, which could mediate the proliferation, migration, and osteogenic differentiation of mesenchymal stem cells (MSCs). The ectopic muscle implant experiments demonstrated that the CaSL-loaded hydrogel scaffolds could stimulate, recruit and capture MSCs and macrophages into scaffolds. The ulnar/cranial bone defect implant results demonstrated that the elasticity of scaffolds and the microenvironment constructed by the CaSL degradation played important roles in mediating the spontaneous growth of the cortical bone.