The disclosure provides a flexible substrate, a manufacturing method thereof, and a flexible display device. The flexible substrate includes a cell and a plurality of liquid crystal molecules disposed in the cell. The cell includes a plurality of sub-pixel display areas arranged in an array and a non-display area disposed outside the sub-pixel display areas. The liquid crystal molecules are disposed in each of the sub-pixel display areas and the non-display area, extending directions of the liquid crystal molecules in each of the sub-pixel display areas are perpendicular to a plane on which the flexible substrate is disposed, and extending directions of the liquid crystal molecules in the non-display area are parallel to the plane on which the flexible substrate is disposed. Risk of damage to electrically driven devices in the flexible display device having the flexible substrate can be reduced. As a result, reliability of products is improved.