Given the aquaculture industry on cultivation and marketing that tends to fresh channels in terms of a pattern of shallow dish economy in Taiwan, the effect from market demands and the controllability of channel vendors is significant. The supply chain must introduce the concept of deep processing with circular economy to create products on the perspective of customer requirements and then the competitive advantage is then bolstered. By using the aquaculture type of goldeneye perch as the study case, this study applies linear programming approach to design deep processing systems with cost effectiveness. Implementation results presented in this work can help decision makers better understand the systematic analysis and potentials for the use of on cost effective analysis for deep processing decision making and research invention for academics.