The aim of this work is to investigate the influence of NaOH pretreatment time on the phases and morphologies of Ti6Al4V substrates and hydroxyapatite (HA) coatings. Ti6Al4V substrates were pretreated with a sodium hydroxide (NaOH) solution for different amounts of time (12, 24, 36, 48, and 60 h). After NaOH pretreatment, a three-dimensional porous network of sodium titanate gel was observed on the Ti6Al4V surface. Subsequently, HA deposition was achieved using the hydrothermal-electrochemical methods, while the electrolyte solution containing NaCl, K2HPO4·3H2O, and CaCl2, was maintained at 120 °C and applied by a constant current density of 1.25 mA/cm2 for 120 min. The results indicate that the growth pattern and micromorphology of the HA coating are all influenced by different pretreatment time. After pretreating Ti6Al4V substrates with NaOH for 12 h, needle-like structures are primarily formed on the HA coating, and some dandelion-like morphologies are presented. During 48 h NaOH solution pretreatment, the dandelion-like structures increase with the increase of time. However, the amount of the dandelion-shaped HA drops slightly, when pretreatment time is longer than 48 h. The orientation index of the (002) plane of HA reaches the minimum when Ti6Al4V substrates are pretreated for 48 h, whereas the crystallinity is the highest for this pretreatment time.