The invention provides a colored film substrate, a manufacturing method thereof and a display device, and relates to the technical field of displaying. As for the display device comprising the colored film substrate, the voltage of a black matrix can be tested through via holes in a substrate body of the colored film substrate and accordingly prevented from being measured in a corner prizing mode, and then damage to the display device is avoided. The colored film substrate comprises the substrate body and the black matrix arranged on the substrate body, and further comprises the via holes formed in non-display areas. When the colored film substrate is seen from one side of the substrate body, the portions, in contact with the via holes, of the black matrix are exposed out of the via holes. The manufacturing method is suitable for manufacturing the colored film substrate and the display device comprising the colored film substrate.