Traditional bone grafting requires an open surgical approach to the graft application sites with the attendant complications of a large surgical scar, increased pain and a longer post-operative recovery. To overcome these limitations, there is a great need for the development of better bone graft substitutes. In this study, we developed a novel injectable system which was a biomimetic bone substitute consisted of Poly (L-lactide-co-ε-caprolactone) (P(LLA-CL)) nanoyarns suspended in type I collagen hydrogel (Col). A dynamic liquid support system was employed to fabricate continuous P(LLA-CL) nanoyarns. The electrospun long nanoyarns were chopped into short nanoyarns before they were incorporated into Col. The result of rheological evaluation showed that the mechanical property of Col was enhanced after the nanoyarns were incorporated into it. The mixture of Col and nanoyarn could be smoothly injected out of 16 gauge needle. In vitro study showed that human mesenchymal stem cells (hMSCs) proliferated well on Col with nanoyarns. Alkaline phosphatase activity and osteocalcin expression of hMSCs on hydrogel with nanoyarns were much higher than those on control groups. This study highlights the potential of using a novel injectable biomimetic scaffold for bone regeneration.