Hydroxyapatite/Chitosan (HAp/CS) bio-coatings were prepared by a novel hydrothermal electrophoretic deposition on CS modified carbon/carbon (C/C) composites in isopropyl alcohol, using sonochemical process resulted HAp nanoparticles as raw material. The influences of hydrothermal temperature on the phase, microstructures and the deposition kinetics of the coatings were investigated. The HAp/CS coatings were characterized by X-ray diffraction (XRD), transmission election microscopy (TEM), Fourier transform infrared (FTIR) spectrum and scanning electron microscope (SEM) analyses. Results showed that with the increase of hydrothermal temperature, the porous structure of the coatings changed from loose combination to close combination, and the cohesive force was enhanced. Kinetics investigations showed that the deposition rate also increased with the increase of hydrothermal temperature. The deposition activation energy of HAp/CS coatings by the hydrothermal electrophoresis deposition process was calculated to be 43.58 kJ/mol.