The invention provides a pixel structure and a manufacturing method thereof. The pixel structure comprises a substrate, an anode electrode layer arranged on the substrate, a plurality of pixel units and a cathode electrode layer; the plurality of pixel units are arranged on the anode electrode layer in a rectangular array, and each pixel unit comprises four sub-pixel units which are arranged in a rectangular array; the emitted colors of two sub-pixel units which face each other and are at the adjacent side of any two adjacent pixel units are the same; and the cathode electrode layer is arranged on the plurality of pixel units. According to the invention, the process capability of a metal photomask and the resolution of the pixel units are improved.