A gas diffusion layer, a manufacturing apparatus and a manufacturing method thereof are provided. The gas diffusion layer having different hydrophilic/hydrophobic structure and channel therein can be manufactured quickly and easily by using a coating mask. The gas diffusion layer is used in various fuel cells to enhance the ability of water management and to solve the problem of flooding at the cathode, the problem of water deficit at the anode, and the problem of gas transfer. The gas diffusion layer includes a gas diffusion medium having a first property and a micro porous layer having a second property. The micro porous layer is formed on one surface of the gas diffusion medium. The micro porous layer has a plurality of channel layers penetrating the gas diffusion medium. One of the first property and the second property is hydrophilic, and the other is hydrophobic.