The embodiments of the invention disclose an array substrate, a manufacturing method thereof, and a display panel. The array substrate comprises a base substrate, and a first conductive layer, an insulating layer and a second conductive layer arranged on the base substrate sequentially, the insulating layer comprising a via hole region, a semi-retaining region outside the via hole region and a full-retaining region encircling the semi-retaining region and the via hole region. Since the via hole region is surrounded by the semi-retaining region, the thickness of the insulating layer around the via hole is reduced, and thus the influence of the material of the insulating layer left on a rim of the via hole can be reduced. Moreover, since the height difference of the insulating layer is divided into two segments, the influence by height difference in the overall thickness of the insulating layer can be diminished.