Bio-ceramic hydroxyapatite (HA) coating has been commonly used to repair the bones or as the functionalized surface of bone substitutes due to its excellent biocompatibility, superior osteo-inductivity, and great corrosion resistance. Among many other methods for synthesizing HA coating, coating via the electrochemical deposition has a high degree of crystallinity and purity, which fits the nonlinear, complex, and rugged substrates. Furthermore, HA coating can be adjusted in terms of coating morphology, thickness, and chemical component via changing the parameters, such as electrolyte ion concentration, electrolyte composition, deposition current density, and deposition time, etc. Nevertheless, the properties of electrodeposited HA coating highly pertain to the bubbles generated by water electrolysis on the substrate surface as well as the concentration polarization of electrolyte ions near the cathode during the electrodeposition process. In this study, the critical factors and mechanisms of HA coating using the electrochemical deposition method are comprehensively evaluated, thereby examining the effects of parameter optimization (i.e., current mode, ultrasonic treatment, and postprocessing). Finally, the influences of ion substitution and HA composite coating on the surface structure and properties of the HA-based coatings are also discussed.