To better mimic the mineral component and the microstructure of natural bone, novel nano-hydroxyapatite (NHAP)/polymer composite scaffolds with high porosity and well-controlled pore architectures were prepared using thermally induced phase separation (TIPS) techniques. The morphologies, mechanical properties and protein adsorption capacities of the composite scaffolds were investigated. The high porosity (90% and above) was easily achieved and the pore size was adjusted by varying phase separation parameters. The NHAP particles were dispersed in the pore walls of the scaffolds and bound to the polymer very well. NHAP/polymer scaffolds prepared using pure solvent system had a regular anisotropic but open 3D pore structure similar to plain polymer scaffolds while micro-hydroxyapatite (MHAP)/polymer scaffolds had a random irregular pore structure. The introduction of HAP greatly increased the mechanical properties and improved the protein adsorption capacity. In a dioxane/water mixture solvent system, NHAP-incorporated poly(L-lactic acid) (PLLA) scaffolds developed a fibrous morphology which in turn increased the protein adsorption three fold over non fibrous scaffolds. The results suggest that the newly developed NHAP/polymer composite scaffolds may serve as an excellent 3D substrate for cell attachment and migration in bone tissue engineering.