The present invention provides a TFT substrate structure and a manufacturing method thereof. In the manufacturing method of a TFT substrate structure according to present invention, a graphene layer is formed on a semiconductor layer and after the formation of a second metal layer, the second metal layer is used as a shielding mask to conduct injection of fluoride ions into the graphene layer to form a modified area in a portion of the graphene layer that is located on and corresponds to a channel zone of the semiconductor layer, wherein the modified area of the graphene layer shows a property of electrical insulation and a property of blocking moisture/oxygen so as to provide protection to the channel zone; portions of the graphene layer that are located under source and drain electrodes are not doped with ions and preserves the excellent electrical conduction property of graphene and thus electrical connection between the source and drain electrodes and the semiconductor layer can be achieved without formation of a via in the graphene layer, making a TFT device so manufactured showing excellent I-V (current-voltage) output characteristics and stability, saving one mask operation process, shortening the manufacturing time, and lowering down the manufacturing cost.