Taking the inspiration from the biomineral, the silk sericin was selected to modulate the assembly of nanosized hydroxyapatite crystals via a modified co-precipitation method. The effect of silk sericin concentration and mineralization time on the formation of hydroxyapatite nanocrystals, including their nucleation, growth, aggregate, especialy assembly dynamic, were investigated using transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), scan electron microscopy (SEM), X-ray diffraction (XRD) and fourier transform infrared (FT-IR) spectroscopy. The results revealed that both the concentration of silk sericin and the mineralization time could influence the size, morphology and assemble of hydroxyapatite crystals. Higher concentration of silk sericin in the reaction system were apt to the formation of larger hydroxyapatite crystals and longer mineralization time was help to improve the crystallinity of hydroxyapatite crystals together with a increase of crystal size. More interested thing was that an arrangement of nanocrystals in order was observed when the concentration of silk sericin was kept at 1% in the reaction system. Larger rod-like hydroxyapatite crystals of 300-500 nm in length and 50-80 nm in diameter was assembled along c-axis by smaller crystals of 20 nm or so under the control of silk sericin, whose arrangment method was similar to the natural enamel. A proposed formation mechanism of the special structure was elucidated. In addition, the biocompatibility of obtained crystals was evaluated in vitro and their stronger ability to promote cell differentiation and proliferation was proved in the paper, which may be important for the biomedical applications and also for the fundamental studies of cell-matrix interactions.