The crystallographic orientation relationship between hydroxyapatite (HAp) nanocrystals and poly (acrylic acid) (PAA) graftpolymer-modified poly (ethylene terephthalate) (PET) substrate was studied using transmission electron microscopy (TEM). We observed the microstructure of fabricated rod-like HAp nanocrystals and the interface of HAp/PET composite where, the HAp nanocrystals are bonded onto PAA graftpolymer-modified PET substrate. The selected-area electron diffraction (SAED) pattern of interface of the HAp/PET composite indicated that some low index planes in HAp prism plane tended to be contact plane with the PET substrate surface. In particular, the {1120} plane was distinctly found as the contact plane with PET substrate. In this material, it has been reported that the carboxyl groups of PAA graft-polymer are ionically-bonded with Ca ions on surface of the HAp nanocrystal. It was suggested that the periodic ionic arrangements of the {1120} plane play an important role on the bonding between the HAp nanocrystals and the carboxyl groups of graft-polymer on the PET substrate.