Bone repair is a complex process involving the sophisticated interplay of osteogenic stem cells, extracellular matrix, and osteoinductive factors, and it is affected by bacterial toxins and oxidative stress. Inspired by the nature of plant‐derived phytochemicals and inorganic–organic analogues of the bone extracellular matrix, herein, the facile design of a nanoclay–organic hydrogel bone sealant (NoBS) that integrates multiple physicochemical cues for bone regeneration into a single system is reported. Assembly of phytochemical‐modified organic chitosan and silica‐rich inorganic nanoclay serves as highly biocompatible and osteoconductive extracellular matrix mimics. The decorated phytochemical exerts inherent bactericidal and antioxidant activities, and acts as an intermolecular networking precursor for gelation with injectable and self‐healing capabilities. Moreover, the NoBS exerts osteoinductive effects mediated by the nanoclay, which regulates the Wnt/b‐catenin pathway, along with the addition of osteoinductive signals, resulting in bone regeneration in a nonhealing cranial defect. Engineering of this integrated bone graft substitute with multifunctional properties inspired by natural materials may suggest a promising and effective approach for creating a favorable microenvironment for optimal bone healing.