The invention provides a manufacturing method of a pixel structure, comprising the following steps: forming a gate on a substrate; forming a gate insulating layer for covering the gate on the substrate; forming a source electrode and a drain electrode above the gate; forming a hydrophobic pattern on the drain electrode; forming a protective layer for covering the source electrode and the drain electrode on the substrate, wherein the hydrophobic pattern is not contacted with the protective layer and forms a contact window opening in the protective layer above the drain electrode; curing the protective layer and removing the hydrophobic pattern; and forming a pixel electrode on the protective layer, wherein the pixel electrode is filled in the contact window opening and electrically connected with the drain electrode. The manufacturing method of the pixel structure is used to simplify the manufacturing process and reduce the manufacturing cost.