Amorphous indium tin oxide (ITO) thin films were deposited on polymethylmethacrylate and poly-ethyleneterephthalate substrates by radio frequency magnetron sputtering at room temperature. An interesting substrate morphology effect of ITO films on the conductivity, optical transition type and energy band structure was observed. A simplified film system model with a square potential for surface morphology was employed to explain the difference of conductivity. The energy band structures were also calculated based on the theory of amorphous semiconductor. The conclusion demonstrated the width of optical band gap, as well as the relative position of the Fermi level and mobility edge, which can easily be extended to the band structure determination of other transparent conductive films.