Maintaining the high crystallinity and tailoring the nano-structured surface of hydroxyapatite (HA) coatings on Ti-6Al-4V implants play critical roles in realizing their long-term service life span and fast osseointegration for biomedical implants. Herein, a nanorod structured HA (nHA) coating with a pure phase and high crystallinity was successfully developed by combining atmospheric plasma spraying (APS) with hydrothermal treatment (HT). The crystallinity degree of the plasma-sprayed HA coating was increased from 51.3% to over 85.3% by hydrothermal treatment, which meets the medical device industrial standard of having a crystallinity no less than 62% and significantly decreased the degradation rate of the HA coating. In addition, the construction of a nanorod structured surface promoted the attachment, proliferation and differentiation of rat bone mesenchymal stem cell (rBMSCs), thus further improving the osseointegration between implants and the surrounding bone tissue. Hence, the stable and bioactive nHA-coated Ti-6Al-4V implant has considerable potential in dental and orthopedic applications.