The present disclosure provides a flexible display device and a manufacturing method thereof. The flexible display device includes a base substrate; a pixel defining layer disposed on the base substrate defining a plurality of light emitting regions; and a first electrode layer disposed on a side of the pixel defining layer away from the base substrate and in light-emitting regions. A thin film encapsulation layer covers the first electrode layer and has protrusions protruding toward the pixel defining layer at a plurality of positions.