A flexible substrate, a manufacturing method thereof, and a flexible display device are provided. The method includes: step S10, forming a first aerogel layer with a cross-linked structure and a nanoporous structure on a substrate; step S20: forming an inorganic layer on the first aerogel layer; step S30, forming a second flexible substrate layer on the first aerogel layer, and allowing the second flexible substrate layer to cover the inorganic layer; and step S40, peeling the first aerogel layer, the inorganic layer, and the second flexible substrate layer from the substrate to form the flexible substrate.