An array substrate, a manufacturing method thereof and a display device are disclosed. The array substrate comprises: a base substrate (1), thin-film transistors (TFTs), an isolation layer (10) and an organic resin layer (8) formed on the base substrate (1), and a common electrode layer (12) formed on the organic resin layer (8). The isolation layer (10) covers source electrodes (6) and drain electrodes (7) of the TFTs; the organic resin layer (8) covers the isolation layer (10) and is provided with first through holes (9) corresponding to the drain electrodes (7) of the TFTs; the isolation layer (10) is provided with second through holes (11) communicated with the first through holes (9) to expose partial drain electrodes (7); and the dimension of the second through holes (11) is greater than that of the first through holes (9). The array substrate, the manufacturing method thereof and the display device resolve the problem of forming dark dots, ensure the product quality, reduce the waste of production materials, and reduce the production cost.