An array substrate and a manufacturing method thereof, a display panel and a display device are disclosed. The method for manufacturing an array substrate includes: forming a first via hole (11) for connecting a second transparent electrically conductive layer (39) and a gate line layer (39), a second via hole (12) for connecting a first transparent electrically conductive layer (30) and the second transparent electrically conductive layer (39), and a third via hole (13) for connecting the second transparent electrically conductive layer (39) and a source/drain electrode layer (34) on a base substrate (10) through patterning process; performing a filling process on the first via hole (11), the second via hole (12) and the third via hole (13) during a pattern of second transparent electrically conductive layer is being formed, such that each of the first via hole, the second via hole and the third via hole which are filled has a top surface which is in the same horizontal plane as portions of the second transparent electrically conductive layer (39) surrounding the respective via holes. The method can reduce the height difference between the top surface of the via hole and the transparent electrically conductive layer surrounding the via hole and to solve the problem of uneven diffusion of the PI orientation layer.