A color filter substrate, a manufacturing method thereof, and a display panel are provided. The color filter substrate includes a color filter layer. The color filter layer includes a plurality of color resist units distributed on a base substrate, and an intersection area is defined between two adjacent color resist units. The color filter layer can be directly used as an electrode on the color filter substrate. That is, when manufacturing the color filter substrate, a step of manufacturing a conductive film layer can be omitted, thereby improving production efficiency of the color filter substrate, and meanwhile reducing production cost of the color filter substrate.