Plasmonic color filters in mass production have been restricted from current fabrication technology, which impede their applications. Soft-X-ray interference lithography (XIL) has recently generated considerable interest as a newly developed technique for the production of periodic nano-structures with resolution theoretically below 4 nm. Here we ameliorate XIL by adding an order sorting aperture and designing the light path properly to achieve perfect-stitching nano-patterns and fast fabrication of large-area color filters. The fill factor of nanostructures prepared on ultrathin Ag films can largely affect the transmission minimum of plasmonic color filters. By changing the fill factor, the color can be controlled flexibly, improving the utilization efficiency of the mask in XIL simultaneously. The calculated data agree well with the experimental results. Finally, an underlying mechanism has been uncovered after systematically analyzing the localized surface plasmon polaritons (LSPPs) coupling in electric field distribution.