Although TiO2 nanotubes is a promising electrode as supercapacitors due to its high energy density, easy synthesis and chemical stability, there are draw backs such as low conductivity and capacitance. Many studies concentrated on improving its electrochemical performance itself but little attention was payed to the reason of capacitance differences caused by its different crystal structures. Herein, we prepare amorphous and anatase TiO2 nanotubes and hydrogenated them by a simple electrochemical hydrogenation method to improve their conductivity and capacitance. And then study and compare their morphology and structure differences by SEM, TEM, XRD and BET. The results show that the pore size distribution, internal structure order and internal carrier concentration are the main reasons for their electrochemical performance differences. The microporous structure less than 2 nm in amorphous nanotubes act as a trap of electrolyte ions at current density larger than 0.1μA cm-2, leading to small charge and discharge capacitance. The long-range ordered crystal structure of anatase is more favorable for the orderly diffusion of carriers, reducing the inelastic scattering of carrier diffusion process and the electron hole-complexing probability, making anatase nanotubes exhibit higher coulomb efficiency and cycle stability than that of amorphous ones.