Biphasic calcium phosphate (BCP) consisting of hydroxyapatite (HAp) and β-tricalcium phosphate is usually prepared by thermal decomposition of calcium-deficient HAp (CDHAp). However, the calcium deficiency and morphology of CDHAp are difficult to manipulate in parallel. In this study, we report a novel strategy for controlling the composition of nanoporous BCP by using only CDHAp nanoparticles with specific properties (Ca/P molar ratio, 1.61; particle size, 50nm) as a building block and by adjusting the calcium deficiency of the nanoparticle-assembled CDHAp (Ca/P molar ratio, 1.50–1.67; pore size, 8nm) with the addition of water-soluble Ca(NO3)2 or (NH4)2HPO4. After thermal treatment at 1000°C, the composition of BCP could be predictably controlled by adjusting the Ca/P ratio of the nanoparticle-assembled CDHAp. Changes in the Ca/P ratio did not significantly affect the surface morphology of BCP, but the grain size (210–300nm) and pore size (140–170nm) tended to increase slightly as the Ca/P ratio decreased. The porosity significantly decreased upon the addition of Ca salts (porosity, 20%) or PO4 salts (porosity, 14%) compared with that of the sample without additives (porosity, 53%). In vitro tests demonstrated enhanced cell adhesion on nanoporous BCP compared with densely sintered pure HAp, and cell differentiation was promoted on the nanoporous pure HAp.