X-ray micro diffractometry, transmission electron microscopy, environmental scanning electron microscopy, energy dispersive spectrometry and Fourier transform infrared were employed to investigate the crystallographic characteristics of the inorganic mineral existing in bones of Cololabis saira. The results show that the crystal phase in hard tissues of Cololabis saira is hydroxylapatite (HAP). Chemical composition analysis reveals that the HAP in hard tissues lacks P and is rich in Ca. Refined lattice parameters of HAP show that a = 0.93622–0.93787 nm and c = 0.68549–0.69011 nm. The domain sizes calculated from the Scherrer equation are 18.9–20.7 nm long along the c-axis and about 6.2 nm thick perpendicular to the c-axis, and is well evidenced by TEM data. The crystallinity of HAP is poor compared with natural HAP. In situ X-ray micro diffraction patterns measured from raw hard tissue show a very strong reflection from the (002) and (004) lattice planes on the cross-section of bone and nearly no reflection from the (002) and (004) lattice planes on elongation surface of bone. Compared with the XRD pattern of standard HAP data and from the textural index R values, it indicates that the HAP in the hard tissues of Cololabis saira has a strong preferring orientation along the crystallographic c-axis. This is verified by Fourier transform infrared on the elongation surface of bone and by selected area electron diffraction of HRTEM on the section perpendicular to elongation of bone. A quantitative textural degree index DR is proposed. The crystallographic characteristics of bio-hydroxylapatites (particle size, crystallinity and preferring orientation) are designed by tissue function and controlled by organic matrix to provide a good mechanical performance.