Most of eco-friendly agrifood processing enterprises in Korean rural area are small and medium-sized business. For this reason, it’s hard for eco-friendly agrifood processing enterprises to neither analyze business performance for efficient business management nor establish their own business plan for rational decision-making. Therefore it’s necessary to design effective mathematical programming model and to make practical application which can support rational management decisionmaking ensuring the stable business activity of eco-friendly agrifood processing enterprises. Accordingly this paper focuses on the designing and its application of multi-objective mathematical programming model using goal programming to support rational decision-making of eco-friendly agrifood processing enterprise. Hansalimanseongmachum Food Inc. which runs soy bean processing business making tofu based on regional-based soybean farms around Anseong City will be the specific case to apply multi-objective mathematical programming model in practice. And it will suggest measures to support rational management decisionmaking of other eco-friendly agrifood processing enterprises.