The invention provides a BCE TFT substrate and manufacturing method thereof. The method comprises forming a first IGZO thin film with polycrystalline IGZO particles in a predetermined area of active layer before sputtering IGZO, the polycrystalline IGZO particles in the first IGZO thin film used as seed crystal during sputtering to grow a C-axis crystallized IGZO in good crystalline state to form a second IGZO thin film. The first and second IGZO thin films form an active layer. Because the surface of the active layer is presented as C-axis crystallized IGZO, the active layer is not damaged by the copper etchant during etching source and drain so as to ensure stable performance of active layer and to avoid the development of special copper etching solution. As such, the BCE TFT substrate has stable electrical performance. The BCE TFT substrate manufactured by the above manufacturing method has stable electrical performance.