A color filter substrate, a manufacturing method thereof, and a display panel are provided. The color filter substrate includes a first substrate, a color resist layer, an overcoat layer, and a quantum dot layer, which are sequentially stacked. The color resist layer includes a plurality of sub-color resist layers with different colors arranged along a second direction, and there is no black matrix disposed between two adjacent sub-color resist layers. The quantum dot layer is divided into a plurality of quantum dot areas arranged along the second direction. A plurality of banks are disposed between and correspond to two adjacent quantum dot areas, and the banks are black.