The embodiment of the invention provides a color film substrate and a manufacturing method thereof and a display panel, which relate to the field of displaying, and can be used for increasing the contrast of a display and further improving the displaying quality of the display. The color film substrate comprises a first transparent electrode layer, a black matrix pattern, uniformly-arranged display units and a second transparent electrode layer, wherein the first transparent electrode layer is positioned on a substrate; the black matrix pattern is positioned on the first transparent electrode layer; the uniformly-arranged display units are formed in a pixel region formed by encircling the black matrix pattern; the second transparent electrode layer covers the display unit and the black matrix pattern; and each display unit comprises a plurality of patterns for displaying sub-pixel material layers of images, and a pattern of an electrochromic display device (ECD) sub-pixel material layer for controlling display contrast. The color film substrate is applied to manufacturing of display panels.