A color filter substrate, a manufacturing method thereof and a display device are provided. The color filter substrate includes a substrate; a black matrix dividing the substrate into a plurality of sub-pixel areas arranged in matrix; a color filter layer including color photoresist patterns with N different colors, N≧3, arranged cyclically in discontinuous sub-pixel areas in adjacent N rows/columns, the color photoresist patterns in M adjacent sub-pixel areas of a single color in at least one line/column in the color filter layer extending to regions over the black matrix corresponding to regions between adjacent sub-pixel areas, to form continuous strip-like color photoresist patterns, wherein M≧2; and spacers including main spacers disposed over regions between adjacent discontinuous color photoresist patterns corresponding to the black matrix and secondary spacers disposed over regions of the continuous strip-like color photoresist patterns corresponding to the black matrix.