Abstract: In order to solve the distribution of hydroxyapatite (HA) in the chitosan (CS) matrix，a novel route of in-situ hydrothermal precipitation was developed to fabricate the nano-HA/CS composites，based on the combination of the advantages of in-situ precipitation and hydrothermal synthesis. The effect of pH value on the structure of the HA/CS composites was studied. All the results show that the as-prepared composites are composed of CS crystals and nano-HA with lower crystallinity，and the growth of CS crystals and HA crystallites is towards the preferred orientation along the c-axis in the crystal structure. Moreover，there is an increase of the crystallinity of CS and HA with the increase of pH value in the composites. It was noticed that the crystallite size of HA and the degree of the ordered arrangement of CS molecules are increased with raising the pH value in the composites. The pH value of 12 is favorable to the formation of the α-CS crystals with higher crystallinity and nano-HA crystallites in these composites. When the composites were prepared at the pH value of 12，there is a more ordered arrangement in the α-CS crystals and the good interaction behavior is found between CS molecules and HA crystallites in the composites.