Well-aligned TiO2 nanorod arrays (TNAs) were prepared on the pretreated quartz substrates. The effect of the pretreatment conditions on the growth of TNAs was systematically investigated by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM) and high-resolution transmission electron microscopy (HRTEM). It is demonstrated that the pre-coating TiO2 crystal seeds on the substrates can greatly improve the growth orientation of TNAs. Rutile Ti02 crystal seeds induce the nucleation and growth of TNAs more preferably than the anatase TiO2 seeds. The growth density and diameter distribution of TNAs strongly depend on the TiO2 crystal seeds density. It is proved that TNAs with different morphologies can be controllably synthesized by using hydrothermal approach by pretreating substrates. The photocatalytic activity of TNAs was investigated by measuring the photodegradation rate of methyl blue aqueous solution under UV irradiation (254 nm). And the results show that TNAs with large growth density and small diameter size exhibit relatively higher photocatalytic activity.