The invention discloses a color box processing system and a color box processing method thereof. The color box processing system comprises a cutting device, a printing system, a surface treatment system, a corrugation mounting device, a box rolling device, an inspection device and a packaging device. The processing process of the color box processing method sequentially comprises the steps of cutting, printing, printing inspection, surface treatment, corrugation mounting, box rolling, forming, full inspection, packaging and warehousing. The printing step comprise the steps of S1, paper tube installation, S2, printing paper positioning, S3, stable paper feeding and S4, printing operation. According to the system and the method, it can be ensured that the printed content is complete, and waste caused by the situation that content is missing or large-area paper is adopted is avoided.