Electrochemical deposition (ED) has been proposed as a low temperature approach for preparing hydroxyapatite (HA) coatings. To overcome the problem of low adhesion, the preparation of thin and low-porosity coatings on Ti substrates pre-treated by micro-arc oxidation (MAO) is a good strategy. In this paper, a thin and dense HA coating was obtained by modifying parameters at pH 6.4, 45 °C, and 0.5 mA·cm−2. The growth behaviours of HA electrodeposited on MAO coatings were investigated by SEM and EDS technology and summarized that the HA was initially generated in the MAO micropores, then covered the entire MAO surface and gradually grew outwards. This growth pattern was also confirmed by ATR-FTIR, XPS, EIS, open potential, and wettability results at different ED cycles. Adjusting 1:1 power-on/off time ratio affected the morphology of HA grown in the pores in the early stage and also increased the interfacial strength, up to 10.69 MPa at duty cycle 12/24.The cross-section of the final specimen was characterised by TEM and EDS, indicating that amorphous layers, nanocrystalline HA, and submicron HA were formed sequentially from the TiO2(Ca)/HA interface outwards. The increase in Ca2+ concentration and the formation of CaO bonds at the interface may be important reasons for the adhesive enhancement. This process provides a strategy to enhance the strength of bioceramic materials on Ti substrates.