In this work, rutile TiO2 nanorod arrays (NRAs) are prepared on TiO2 seeding/FTO substrates by a hydrothermal process. The synthetic recipe is systematically studied to probe the morphology-synthesis interactions. Results indicate that increasing the seeding thickness greatly improves the uniformity of the top NRAs, and the initial growth for nanorods can be classified into three steps, i.e., nucleation, plant-shaped growth and array-appearance formation. The structural study suggests that each TiO2 nanorod is in fact closely-stacked by many tiny secondary nanorods parallel to each other, which could be opened by a chemical etching process. Upon etching, the performance of dye-sensitized solar cells (DSSCs) based on TiO2 NRAs is substantially improved. The device efficiency achieves a highest value of 4.46% using a 14μm NRAs etched for 3h. The charge dynamics of DSSCs was further investigated by intensity-modulated photocurrent/photovoltage spectroscopy, electrochemical impedance spectroscopy and open-circuit voltage decay. Results show that the electron collection efficiency in the TiO2 NRAs is greatly enhanced after etching, mainly due to the retarded charge recombination, which is probably induced by the morphology change of the etched NRAs. The present study reveals some important issues for growth of rutile TiO2 NRAs on seeded FTO substrates, introduces a novel etching way for improving charge collection in semiconductor NRAs, and would advance the applications of TiO2 NRAs in various areas, such as solar cells, sensors and batteries.