The disclosure provides an array substrate, a manufacturing method thereof and a display panel, and relates to the technical field of display. The array substrate comprises a first transistor arranged on one side of a substrate base, the first transistor being located in an active area of the array substrate; a flat layer covering the first transistor, the flat layer having a first through-hole; a first electrode layer arranged in the first through-hole, and being connected with a drain of the first transistor and having a first groove; a filling layer arranged in the first groove; and a second electrode layer arranged on a side, away from the first transistor, of the filling layer, the second electrode layer being connected with the first electrode layer. So an electric field for driving a liquid crystal layer is more uniform, thereby improving an aperture ratio of the display panel.