A method of fabricating a pixel structure is disclosed. A substrate having a color filter layer thereon and a leveling layer further covers the color filter layer is provided. A first metal layer is formed over the leveling layer. The first metal layer is patterned to define a source/drain. A channel material layer, a gate insulating layer and a second metal layer are formed over the substrate to cover the source/drain. The second metal layer, the gate insulating layer and the channel material layer are patterned to define a gate and a channel layer. A passivation layer is formed over the substrate to cover the gate. The passivation layer is patterned to expose a portion of the drain. A transparent conductive layer is formed over the substrate, and is electrically connected to the exposed drain. Thereafter, the transparent conductive layer is patterned to form a pixel electrode.