Silk (SF)-based hydrogels have widely developed for various biomedical applications including tissue engineering, drug delivery, ect. However, current methods for SF gelation showed significant limitations such as use of nonphysiological conditions, lack of reversible crosslinking, and difficulties in controlling gelation time. In this study, we used dynamic metal-ligand coordination chemistry approach to develop SF-based hydrogel based on SF microfibers (mSF) and a polysaccharide binder under physiological conditions. The presented SF-based hydrogel showed self-healing and shear-thinning properties that give the advantages for the filling of irregularly shaped tissue defects without gel fragmentation. We used biomineralization approach to generate calcium phosphate-coated mSF (CaP@mSF). The hydrogel could be formed by simply mixed the polysaccharide binder and CaP@mSF basing on the reversible cross-linkages between bisphosphonate ligands on the backbone of the binder and the CaP on the mineralized mSF. Robust dually crosslinked (DC) hydrogel was obtained by photopolymerization of acrylamide groups of the binder. The DC SF-based hydrogel not only supported mesenchymal stem cell proliferation in vitro but also accelerated bone regeneration in rat cranial critical size defect model even without any additional growth factors delivered. Therefore, the developed self-healing and photopolymerizable SF-based hydrogel have significant potential as injectable bone regeneration scaffolds with the advantages of fit-to-shape molding.