Recent studies suggest that nanotopography can trigger colocalization of integrins and bone morphogenetic protein 2 (BMP2) receptors (e.g., BMPR1A), thereby leading to osteogenesis. In this study, the bone marrow homing peptide 1 (BMHP1) motif was bound to a self-assembling peptide core to form a hydrogel-based nanofiber (R-BMHP1). The docking and molecular dynamic study revealed that the R-BMHP1 sequence induced a stronger electrostatic interaction than BMP2 through arginines in the RADA core sequence and through lysine24 in the BMHP1 motif with BMPR1A. Notably, decrease of polar solvation binding energy will enhance the total binding energy and increases bone regeneration even more than BMP2 The enhanced osteogenesis and bone repair potential of R-BMHP1 nanofiber might be related to its chemical interaction with BMPR1A, which triggered downstream signal transduction through osteogenic genes overexpression in osteo-differentiated mesenchymal stem cells (MSCs), as well as implanted critical-sized bone defects in rats. Following that, calcium deposition occurred by osteoblast-like cells, ALP activity increased in osteodifferentiation MSCs and rat serum, and calcium density improved in bone defects (X-ray). The nanofiber was biocompatible and enhanced the cell viability of MSCs, without multinuclear cell infiltration into the defect site. Taking everything into account, not only does nanotopography induce osteogenesis through colocalization of BMPRs and integrins, but also R-BMHP1 nanofibers (considering their chemical structure) induce cell proliferation, osteogenesis, and bone repair through strong electrostatic interaction with BMPR1A and downstream signaling. The entire outcome of this study manifests the plausibility of R-BMHP1 for spine and spinal cord injury repair.