Abstract: Based on grey system, this paper established an input-output optimization model, and the model was used to analyze the input-output of aquaculture. After gotten the coefficients of inputs and outputs of aquaculture, using GM (1,1) model we could predict the final demand for aquaculture (upper and lower), the resource level of assurance (maximum-minimum volume); then through qualitative analysis and quantitative research, the future input-output coefficients for each phase was revised and the grey input-output model would be designed; Finally, using model calculations, we could obtain various options. After the comprehensive demonstration, we could get the most satisfactory solution. From the numerical results, the model could complement each other, quick to solve and make Grey Target decision easily.