A roll-to-roll manufacturing system performs printing and coating on webs to mass-produce large-area functional films. The functional film of a multilayered structure is composed of layers with different components for performance improvement. The roll-to-roll system is capable of controlling the geometries of the coating and printing layers using process variables. However, research on geometric control using process variables is limited to single-layer structures only. This study entails the development of a method to proactively control the geometry of the upper coated layer by using the lower-layer coating process variable in the manufacture of a double-coated layer. The correlation between the lower-layer coating process variable and upper coated layer geometry was examined by analyzing the lower-layer surface roughness and spreadability of the upper-layer coating ink. The correlation analysis results demonstrate that tension was the dominant variable in the upper coated layer surface roughness. Additionally, this study found that adjusting the process variable of the lower-layer coating in a double-layered coating process could improve the surface roughness of the upper coating layer by up to 14.9%.