A method of manufacturing a pixel structure includes: forming a source, a drain and a first capacitor electrode; forming a semiconductor layer in contact with a portion of the source and a portion of the drain; forming a gate and a second capacitor electrode, and the second capacitor electrode substantially aligned with the first capacitor electrode; forming a gate insulating layer between the semiconductor layer, the source, the drain and the first capacitor electrode, and the gate and the second capacitor electrode; forming a passivation layer over the source, the drain, the first capacitor electrode, the semiconductor layer, the gate and the second capacitor electrode; and forming a pixel electrode over the passivation layer, and the pixel electrode substantially aligned with the first capacitor electrode.