The printing process can have to print various colors with a limited capacity of printing facility such as ink containers that are needed cleaning to change color. In each container, cleaning time exists to assign corresponding inks, and it is considered as the setup cost required to reduce the increasing productivity. The existing manual method, which is based on the worker’s experience or intuition, is difficult to respond to the diversification of color requirements, mathematical modeling and algorithms are suggested for efficient scheduling. In this study, we propose a new type of scheduling problem for the printing process. First, we suggest a mathematical model that optimizes the color assignment and scheduling. Although the suggested model guarantees global optimality, it needs a lot of computational time to solve. Thus, we decompose the original problem into sequencing orders and allocating ink problems. An approximate function is used to compute the job scheduling, and local search heuristic based on 2-opt algorithm is suggested for reducing computational time. In order to verify the effectiveness of our method, we compared the algorithms' performance. The results show that the suggested decomposition structure can find acceptable solutions within a reasonable time. Also, we present schematized results for field application.