A method of manufacturing a TFT substrate includes: sequentially forming a transparent conductive layer and an opaque conductive layer on a substrate, patterning the transparent conductive layer and the opaque conductive layer by using a first mask to form a gate pattern including a pixel electrode, and forming a gate insulating layer and a semiconductor layer above the substrate. A contact hole is formed which exposes a portion of the pixel electrode and a semiconductor pattern using a second mask. A conductive layer is formed above the substrate and patterned to form a source/drain pattern including a drain electrode which overlaps a portion of the pixel electrode. Portions of the gate insulating layer and the opaque conductive layer above the pixel electrode are removed except a portion overlapping the drain electrode, by using a third mask.