In a method of manufacturing a thin film transistor substrate, a gate line and a gate electrode are formed on a substrate. A gate insulating layer is formed to cover the gate line and the gate electrode. A semiconductor layer is formed on the gate insulating layer to overlap with the gate electrode. A data line, a source electrode, and a drain electrode are formed on the gate insulating layer and the semiconductor layer. A photoresist layer is formed on the data line, the source electrode, and the drain electrode. The photoresist layer is patterned, and an organic layer is formed on the substrate having the photoresist layer pattern. Then, the photoresist layer pattern is removed.