Aggregation of titania nanotubes (TNTs) fabricated by hydrothermal method were calcined in air and dry nitrogen; Changes in morphology and crystallinity of the nanotubes were studied by means of TEM, EDX, and XPS. EDX patterns and XPS spectra proved that there were a certain densities of oxygen vacancies in TNTs annealed in $N_2$. The photocatalysis experiments revealed TNTs/$N_2$ possesses significantly higher photocatalytic efficiency than TNTs annealed in dry air to degrade methylene blue. The correlation between oxygen vacancies and photocatalytic property may be attributed to: 1) oxygen vacancies might have affected results on water molecules adsorption and increase of the hydroxyl concentration; and 2) oxygen vacancies resulted in some changes in electronic structure of TNTs/$N_2$ aggregation and Fermi level extends into the conducting band.