A high-performance multilayer coating with external, flexible, and silicon-doped hydroxyapatite (Si-HA) nanorods was designed using bionics. Plasma electrolytic oxidation (PEO) and the microwave hydrothermal (MH) method were used to rapidly deposit this multilayer coating on a titanium (Ti) substrate, applied for 5 and 10 min, respectively. The bioactive multilayer coating was composed of four layers, and the outermost layer was an external growth layer that consisted of many Si-HA nanorods with a singlecrystal structure. The Si-HA nanorods exhibited good flexibility, likely because of their complete single-crystal structures, smooth surfaces, and suitable diameters and lengths. This multilayer coating with a high surface energy was superhydrophilic and exhibited good in vitro bioactivities, such as good apatite formation ability, good cell spreading, and high osteogenic gene expression levels. After implantation in the tibia of rabbits for 16 weeks, almost no soft tissues were formed at the MH treated PEO implant-bone interface. A direct bone contact interface was formed by a bridging effect of the flexible Si-HA nanorods, which further produced a high implant-bone interface bonding strength. The current results demonstrated that the bioactive multilayer layers with the flexible Si-HA nanorods displayed a very good osseointegration ability, showing promising applications in the biomedical field.