A flexible base substrate, a manufacturing method thereof, and a display device are provided. The flexible base substrate includes a first flexible substrate. The first flexible substrate includes: a first flexible film layer including a flexible film layer body, and a plurality of protrusions spaced apart from each other on a surface of a side of the flexible film layer body; a first spacer layer on the first flexible film layer and including a plurality of first islands spaced apart from each other; and a first groove between adjacent first islands. The first groove is filled with a first organic material, and a height of the first organic material is smaller than a height of the first groove in a direction perpendicular to the flexible film layer body.