The worldwide incidence of bone disorders has trended steeply upward and is expected to get doubled by 2030. The biological mechanism of bone repair involves both osteoconductivity and osteoinductivity. Despite the self-healing functionality after injury, bone tissue faces a multitude of pathological challenges. Several innovative approaches have been developed to prepare biomaterial-based bone grafts. To design a suitable bone material, the freeze-drying technique has achieved significant importance among the other conventional methods. However, the functionality of the polymeric freeze-dried scaffold in in-vivo osteogenesis is in a nascent stage. In this study facile, freeze-dried, biomaterial-based load-bearing three-dimensional porous composite scaffolds have been prepared. The biocompatible scaffolds have been made by using chitosan (C), polycaprolactone (P), hydroxyapatite (H), glass ionomer (G), and graphene (gr). Scaffolds of eight different groups (C, P, CP, CPH, CPHG, CPHGgr1, CPHGgr2, CPHGgr3) have been designed and characterized to evaluate their applicability in orthopedics. To evaluate the efficacy of the scaffolds a series of physio-chemical, morphological, and in-vitro and in-vivo biological experiments have been performed. From the obtained results it was observed that the CPHGgr1 is the ideal compatible material for Wharton’s jelly-derived mesenchymal stem cells (MSCs) and the blood cells. The in-vitro bone-specific gene expression study revealed that the scaffold assists MSCs osteogenic differentiation. Additionally, the in-vivo study on the mice model was also performed for a period of four and eight weeks. The subcutaneous implantation of the designed scaffolds did not show any altered physiological condition in the animals, which indicated the in-vivo biocompatibility of the designed material. The histopathological study revealed that after eight weeks of implantation, the CPHGgr1 scaffold supported significantly better collagen deposition and calcification. The facile designing of the CPHGgr1 multicomponent nanocomposite provided an osteo-regenerative biomaterial with desired mechanical strength as an ideal regenerative material for cancellous bone tissue regeneration.