The invention provides a manufacturing method of a TFT (Thin Film Transistor) substrate, and a TFT substrate. The manufacturing method of a TFT substrate includes the steps: setting first and second color resistance blocks at adjacent color resistance block units in a color resistance block layer and setting a groove in the second color resistance block to enable a flat layer formed on the color resistance block layer to form first and second flat layer bulges, corresponding to the first and second color resistance blocks, wherein the height of the first flat layer bulge is greater than the height of the second flat layer bulge; utilizing a photomask which is provided with a transparent area corresponding to a color resistance block unit boundary area to form a BPS (Black Photo Spacer) light shield layer on the flat layer, wherein the light transmittance in the transparent area is the same; and in the BPS light shield layer, forming a main spacer and an auxiliary spacer which are different in the height on a black matrix, corresponding to the first and second color resistance blocks, wherein the light exposure during the process of manufacturing the black matrix, the main spacer and the auxiliary spacer is the same. The manufacturing method of a TFT substrate enables the height of the black matrix, the height of the main spacer and the height of the auxiliary spacer to have relatively higher homogeneity by improving the light transmittance of the transparent area of the photomask, and can improve the quality of products.