A pixel structure and a fabrication method thereof are provided, and the fabrication method includes steps as follows. A gate and a scan line connected to the gate electrode are formed on a substrate. An insulation layer is formed on the substrate and is patterned to form an opening corresponding to the gate electrode. A gate insulation layer is formed to cover the gate electrode and the scan line. A channel layer is formed on the gate insulation layer and is located in the opening. A first ohmic contact layer and a second ohmic contact layer are formed on the channel layer and are located in the opening. A source electrode, a drain electrode and a data line connected to the source electrode are formed on the first ohmic contact layer and the second ohmic contact layer. A first electrode is formed and is electrically connected to the drain electrode.