A manufacture method of a pixel structure is provided. A gate is formed over a substrate, and a gate insulator layer is formed over the substrate covering the gate. A semiconductor layer is formed over the gate insulator layer and a metal layer is formed over the semiconductor layer. A first mask layer is formed on the metal layer, and the metal layer is patterned to form a source/drain by using the first mask layer as etching mask. Afterward, a second mask layer is formed on the first mask layer and further covers a region between the source/drain. The semiconductor layer is patterned by using the first and second mask layers as etching mask, and then the first and second mask layers are removed. A passivation layer is formed over the substrate. A pixel electrode is formed on the passivation layer. The pixel electrode is electrically connected with the drain.