Self-aligned titania thin films of either the rutile or the anatase phase were successfully grown on FTO (F-doped SnO2) substrates with hydrothermal methods. The selection of the targeted phase, either rutile or anatase, in the thin films was controlled by adjusting the content and type of acidic anions such as Cl− and SO42−. The growth kinetics depended on the synthesis temperature and the types of alcohol in the solvent. The self-alignment in both the anatase and rutile thin films was attributed to the minimization of surface energies during growth. The hydrogen sensing characteristics of dense films of both rutile and anatase phases were investigated and there was remarkable improvement of sensitivity response over reported data. It was found that rutile films had higher sensitivity while anatase films had faster response.