A special three-layer TiO2 nanotube array has been successfully fabricated. The upper and lower porous layers were formed in the same fluoride-containing electrolyte, while the middle barrier layer was formed in fluoride free electrolyte. By changing the applied voltage of middle barrier layer, the growth process of the lower layer was explored and compared systematically. The results show that at a critical voltage of barrier layer, the lower layer could barely be seen. Below the critical voltage, complete three-layer TiO2 nanotubes were achieved, but above the critical voltage, the lower layer failed to appear. Furthermore, some cavities inside the barrier layer were obtained under higher voltage of barrier layer and the conventional three-stage current-time curves were transformed into four-stage curves. Based on the oxygen bubble mould and electronic current model, an explanation for the formation of cavities is firstly proposed.