Through combining the cultivation of milkfish with Gracilaia and oyster, we have successfully established integrated multi-trophic aquaculture (IMTA) system. Furthermore, photosynthesis bacteria were used to improve the water quality and the goal of zero-water exchange was reached during the milkfish culture period. After 25 days of rearing, the growth in weight (total length) of milkfish increase from 32.03 g to 118.01 g (16.28 cm to 22.36 cm) and the specific growth rate is 5.82%. Finally, 1072.8kg of milkfish was harvested. Additionally, the feed for green aquaculture was developed, and feed conversion ratio (FCR) of the milkfish could reach to 1.75. Comparing with the commercial milkfish feed, the cost could be reduced about 2 NT dollars per kg.