The present invention relates to a color film substrate, a manufacturing method thereof, and a display device. The color film substrate comprises m columns of list-structured sub-pixels and n columns of island-structured sub-pixels, wherein m>=1, and n>=1; a first black matrix is disposed between the adjacent rows of the list-structured sub-pixels, and the list-structured sub-pixels cover the first black matrixes; a second black matrix is disposed between the adjacent rows of the island-structured sub-pixels; main spacers are arranged on the list-structured sub-pixels on the first black matrixes; and the auxiliary spacers are arranged on the second black matrixes. According to the technical scheme, the main spacer and the auxiliary spacer having the same height can be formed through the same equipment or technology, due to the fact that the base of the main spacer is higher than the base of the auxiliary spacer, an upper surface of the main spacer is higher than an upper surface of the auxiliary spacer, so that the technology of manufacturing the main spacer and the auxiliary spacer is simplified when the height difference between the upper surfaces of the main spacer and the auxiliary spacer is ensured.