The invention provides a back channel etching type TFT substrate and a manufacturing method thereof. According to the manufacturing method of the back channel etching type TFT substrate provided by the invention, a first IGZO thin film formed by polycrystal IGZO particles is formed in an active layer predetermined region before IGZO sputtering is performed; the polycrystal IGZO particles in the first IGZO thin film are used as seed crystals in the sputtering process to form C-axis crystallization IGZO with high crystallization state to form a second IGZO thin film; the second IGZO thin film and the first IGZO thin film jointly form an active layer; the surface of the active layer is represented by the C-axis crystallization IGZO, so that in the etching process of a source and a drain, theactive layer is not damaged by a copper etching liquid, thereby ensuring performance stability of the active layer, avoiding development of a special copper etching liquid, and enabling the prepared back channel etching type TFT substrate to have stable electrical performance; and the back channel etching type TFT substrate is prepared by adopting the abovementioned manufacturing method and has stable electrical performance.