Multi-walled carbon nanotubes (MWNTs) reinforced hydroxyapatite (HA) composite was fabricated by in-situ method and followed by hot-pressing sintering; the influence of MWNTs’ content on the mechanical and microstructure properties was explored. The results show that adding MWNTs within a certain range could enhance the mechanical properties of HA matrix significantly. The maximal increment of the bending strength and fracture toughness of the composites, compared with the pure HA, were 157% and 171% respectively. XRD and TEM showed that the primary crystal phase of the composite was HA together with the diffraction peaks of carbon nanotube. By SEM, we found that MWNTs are homogeneously dispersed within grains or at grain boundaries of the HA matrix in composites which MWNTs’ content was not more than 15vol%, otherwise MWNTs tended to be agglomerated. The reinforcement mechanism was discussed based on the microstructure investigation. The broken nanotubes and pullout of MWNTs at interfaces were efficient in transferring the load from the HA matrix to the nanotubes, leading to the improvement of the mechanical properties.