A pixel structure and a manufacturing method thereof and a display panel are provided. An electrode material layer, a shielding material layer, an inter-layer dielectric material layer, a semiconductor material layer and a photoresist-layer are sequentially formed on a substrate. The semiconductor material layer, the inter-layer dielectric material layer, the shielding material layer and the electrode material layer are patterned using the photoresist-layer as a mask to form a semiconductor pattern, an inter-layer dielectric pattern, a shielding pattern and a pixel electrode. A source/drain electrically connected to the pixel electrode and covering a portion of the semiconductor pattern is formed on the pixel electrode. A channel is another portion of the semiconductor uncovered by the source/drain. A dielectric layer covering the source/drain, the semiconductor pattern, the inter-layer dielectric pattern, the shielding pattern and the pixel electrode and a gate disposed on the dielectric layer above the channel are formed.