The invention provides a flexible TFT substrate and manufacturing method thereof. The method forms a flexible base and a first organic layer on rigid substrate and forms a plurality of grooves, manufactures TFT devices in the grooves and forms a second organic layer on the first organic layer, finally peels the flexible base from the rigid substrate to obtain a flexible TFT substrate, wherein because a plurality of grooves is disposed in the first organic layer, a plurality of recessed structures and raised structures are formed on the first organic layer so that the second organic layer and the first organic layer are engaged with each other and bonded tightly, and protects the TFT devices sandwiched between the two to prevent the breaking wires, TFT peeling, and leaking light in the bending process, to enhance the flexible TFT substrate quality to prolong the lifespan of flexible TFT substrate.