The invention discloses a production system of low- chromaticity C5/C9 copolymerization hydrogenation resin and a method and belongs to the technical field of hydrogenation of resin. The system comprises a raw material pretreatment device, a copolymerization reactor device, a termination reaction device, a sample feeding and pretreating device, a hydrogenation reaction device and an after-treatment device which are successively connected with each other, wherein the raw material pretreatment device comprises a C5 petroleum resin raw material pretreatment reactor and a C9 petroleum resin raw material pretreatment reactor; the C9 petroleum resin raw material pretreatment reactor is a fixed-bed reactor filled with a high-capacity sulfur-nickel based catalyst; the outlet of the C9 petroleum resin raw material pretreatment reactor is connected with a cooling device. Through the adoption of self-developed process flow and reaction equipment, nonferrous groups of the raw material can be removed; the polymerization process and the hydrogenation process of the petroleum resin raw material are integrated; the system process is simple to operate; the consumption of the catalyst is low; the resin product is high in quality and low in chromaticity.