A color filter (CF) substrate, a manufacturing method thereof and a display panel are provided. The manufacturing method of the substrate includes: providing a base substrate; and forming a black matrix layer and a plurality of first sub-pixel units on the base substrate, wherein the black matrix layer and the plurality of first sub-pixel units are made of photoresist of a same material, the material of the photoresist includes an irreversible thermochromic pigment, the photoresist is changed into black color upon being heated, and a color of the photoresist before color change is the same as a color of the first sub-pixel units.