The embodiment of the invention relates to the field of semiconductors, and discloses a hydrophobic membrane structure, a detection method and a detection system thereof, and a wafer carrier. The hydrophobic membrane structure provided by the invention comprises a color-changing layer and a hydrophobic layer covering the surface of the color-changing layer; and when the color-changing layer is in contact with liquid, the color of the area, in contact with the liquid, of the color-changing layer changes to form a color-changing area. Compared with the prior art, according to the embodiment, the hydrophobic layer covers the surface of the color-changing layer, when the hydrophobic layer is broken, liquid flows into the color-changing layer through the broken area of the hydrophobic layer, and the color of the color-changing layer changes due to the fact that the color-changing layer makes contact with the liquid. Therefore, in the detection process of the hydrophobic membrane structure, whether the hydrophobic membrane structure is damaged or not is detected through the change of the color, so that the hydrophobic membrane structure is replaced in time, and the problem that the hydrophobic membrane structure is damaged only when a product or equipment goes wrong is solved.