The fabrication of bone scaffolds with interconnected porous structure, adequate mechanical properties, excellent biocompatibility and osteoinductivity presents a great challenge. Herein, a hybrid nanostructured hydroxyapatite-chitosan (HA-CS) composite scaffold has been fabricated according to the following steps: (i) the deposition of brushite-CS on a CS fibre porous scaffold by a dip-coating method; and (ii) the formation of a hybrid nanostructured HA-CS composite scaffold by the in situ conversion of brushite to HA using a bioinspired mineralization process. The hybrid HA-CS composite scaffold possesses three-dimensional (3D) interconnected pores with pore sizes of 30-80 μm. The HA rods with a length of ∼200 nm and width of ∼50 nm are perpendicularly oriented to the CS fibres. Interestingly, the abovementioned HA rods are composed of many smaller nanorods with a length of ∼40 nm and width of ∼10 nm oriented along the c-axis. The hybrid nanostructured HA-CS composite scaffold exhibits good mechanical properties with a compression strength of 9.41 ± 1.63 MPa and an elastic modulus of 0.17 ± 0.02 GPa, which are well-matched to those of trabecular bone. The influences of the hybrid HA-CS composite scaffold on cells have been investigated using human bone marrow stem cells (hBMSCs) as cell model and the CS fibre porous scaffold as the control sample. The hybrid HA-CS composite scaffold not only supports the adhesion and proliferation of hBMSCs, but also improves the osteoinductivity. The alkaline phosphatase activity and mineralization deposition on the hybrid HA-CS composite scaffold are higher than those on the CS fibre porous scaffold. Moreover, the hybrid HA-CS composite scaffold can promote the formation of new bone in rat calvarial defects as compared with the CS fibre porous scaffold. The excellent biocompatibility, osteoinductivity and mechanical properties suggest that the hybrid nanostructured HA-CS composite scaffold has great potential for bone tissue engineering.