To serve as carriers of cells and bioactive molecules, three-dimensional scaffolds play a key role in bone defect repair. The chemical component and microstructure of the scaffold can affect the mechanical properties and seed cells. A variety of fabrication techniques have been used in producing scaffolds, some made random porous structure, some created well-designed structure using rapid prototyping methods, and others prepared bio-derived materials as scaffolds. However, scaffolds may vary in their inner structure, mechanical properties and repairing efficiency as well because of different manufacturing methods. In this review, we overview the main achievements concerning the effects of material and microstructure on the mechanical performance, seed cells and defect repair of bone scaffolds.