Physical properties of scaffolds such as nanofibers and aligned structures have been reported to exert profound effects on the growth and differentiation of stem cells due to their homing-effect features and contact guidance. However, the biological function of aligned nanofibers utilized as bone-scaffold has not been rigorously characterized. In the present study, aligned electrospun cellulose/CNCs nanocomposite nanofibers (ECCNNs) loaded with bone morphogenic protein-2 (BMP-2) were used for the first time to investigate (1) in vitro osteogenic differentiation of human mesenchymal stem cells (BMSCs) and (2) in vivo collagen assembly direction and cortical bone regeneration. Aligned ECCNNs scaffolds loaded with BMP-2 possess good biological compatibility. The growth orientation of BMSCs followed the underlying aligned nanofiber morphology, accompanied with increased alizarin red stain, alkaline phosphatase (ALP) activity and calcium content in vitro while, a rabbit calvaria bone defect model was used in an in vivo study with micro CT and histology analyses.