MoO₃ nanorods with well-defined crystalline structure have been grown in situ on Fluorine doped Tin Oxide glass (FTO) by magnetron sputtering and subsequent oxidation treatment. Moreover, the morphologies and the crystalline structures of MoO₃ products could be rationally tailored by adjusting the annealing temperature. More specifically, the calcination operated at 500 °C for 6 h leads to the formation of uniform MoO₃ nanorods with an average diameter of 200 nm, and length of up to 800 nm, whereas only irregular nanoparticles or nanoplates have been obtained when the temperature was higher or lower than 500 °C.