In this paper, we describe three-dimensional (3D) hierarchical graphene–hydroxyapatite hybrid bioscaffolds (GHBs) with a calcium phosphate salt electrochemically deposited onto the framework of graphene foam (GF). The morphology of the hydroxyapatite (HA) coverage over GF was controlled by the deposition conditions, including temperature and voltage. The HA obtained at the higher temperature demonstrates the more uniformly distributed crystal grain with the smaller size. The as-prepared GHBs show a high elasticity with recoverable compressive strain up to 80%, and significantly enhanced strength with Young’s modulus up to 0.933 MPa compared with that of pure GF template (~7.5 kPa). Moreover, co-culture with MC3T3-E1 cells reveals that the GHBs can more effectively promote the proliferation of MC3T3-E1 osteoblasts with good biocompatibility than pure GF and the control group. The superior performance of GHBs suggests their promising applications as multifunctional materials for the repair and regeneration of bone defects.