A TFT substrate and a method of manufacturing the TFT array substrate are disclosed. The method includes providing a substrate, forming an organic layer on the substrate, forming a first transparent conductive layer on the organic layer, and forming a photolithography layer on the first transparent conductive layer, where the photolithography layer has an opening. The method also includes patterning the first transparent conductive layer to form a first via hole in the first transparent layer using the photolithography layer as a mask, where the first via hole is aligned with the opening in the photolithography layer, and patterning the organic layer to form a second via hole in the organic using the photolithography layer as a mask, where the second via hole is aligned with the opening in the photolithography layer.