Oxygen vacancy (OV) controlled hydrophobicity of self-assembled TiO2 nanorods (NRs) on chemically etched Si pyramids is investigated by irradiating with 50 keV Ar+-ions at room temperature. Apparent contact angle (CA) is found to increase from 122° to 141° up to a fluence of 1 × 1015 ions/cm2, followed by a gradual reduction to 130° at 1 × 1017 ions/cm2. However, the drop in apparent CA is found to be associated with the decrease in fractional surface area via transformation of NRs to an amorphous layer above 1 × 1015 ions/cm2, though it is still higher than that of as-grown one. Detailed X-ray photoelectron spectroscopy and electron paramagnetic resonance measurements suggest that the control of hydrophobic behavior is related to the suppression of surface free energy via migration of OVs into the voids in TiOx layers. © 2016 American Chemical Society.