The morphological differences of chitosan (CS) in the hydroxyapatite (HA)/CS nanocomposites were investigated in detailed, which were prepared via in situ hydrothermal precipitation. The results show that the obtained nanocomposites have excellent crystallinity and the crystal has excellent ordered structure, which is important to the composites performances in the biomedical application. Moreover, the CS arrangement and crystallinity in the composites greatly depend on the hydrothermal temperature and the pH value of precipitating agent. The temperature ranging from 373 to 413K and pH value of precipitating agent ranging from 12 to 14 were favorable to the crystallization and oriented growth of CS molecules in the composites. The CS crystals with better arrangement are assembled in the order of layer-by-layer in these composites.