A thin film transistor substrate and a method of manufacturing the thin film transistor substrate comprises forming a gate line and a data line intersecting each other with a gate insulating layer interposed and defining a pixel area on the substrate, a thin film transistor electrically connected to the gate line and the data line, and a stepped-structure occurring pattern overlapping at least one of the gate line and the data line; forming a passivation layer having a stepped-structure portion formed by the stepped-structure occurring pattern on the substrate; forming a photoresist pattern having a second stepped-structure portion corresponding to the stepped-structure portion on the passivation layer; patterning the passivation layer using the photoresist pattern as a mask; forming a transparent conductive layer on the substrate; and removing the photoresist pattern where the transparent conductive layer is covered by a stripper penetrating through the stepped-structure portion of the photoresist pattern and forming a pixel electrode connected to the thin film transistor.