Facilitated endogenous tissue engineering is emerging as a convenient and easy strategy for bone repair. However, the substitution with satisfactory bioactivity and osteoinductivity which can activate endogenous stem cells responds and in situ recruit them homing towards to damaged area remains a challenge. To stimulate the biomineralization process of inorganic nanoparticles in natural bone, bioactive nano hydroxyapatite particles (nHAP) were in situ crystallized into the graphene oxide/chitosan/nHAP (GO/CS/nHAP) scaffold via effective regulation of CS functionalized with GO network matrix and presented a uniform dispersion with nanometer-scale. As-prepared scaffold exhibited better physicochemical properties, such as three-dimensional (3D) porous bone-like hierarchical structure, proper mechanical property, biodegradation as well as suitable water uptake and retention ratio. The biomimetic mineralization and cell culture experiments demonstrated that hybrid scaffold possessed superior bioactivity and cell proliferation ability in vitro. In addition, the rat calvarial defect repair models and tissue pathological characterization further proved that the hybrid scaffold had excellent biocompatibility and capacity of in situ inducing bone regeneration. Herein, the prepared scaffold might be an excellent candidate for endogenous bone repair.