Through combining the cultivation of milkfish with Gracilaia and oyster, the integrated multi-trophic aquaculture (IMTA) systems were established. Furthermore, photosynthesis bacteria were used to improve the water quality. A total of secondary stocking were in these systems. After 20 days of rearing, the growth in weight (total length) of the first stocking milkfish increase from 36.97 g to 91.79 g (16.41 cm to 21.54 cm), and 917.2 kg of milkfish was harvested. Then, total weight 987.0 kg of the secondary stocking milkfish was harvested after 26 days breeding, and the growth in weight (total length) increase from 42.11 g to 97.83 g (16.74 cm to 21.74 cm). However, the feed for green aquaculture was developed, and feed conversion ratios (FCR) of the milkfish were 2.66 and 2.86. Finally, during the period of experiments, pH, temperature, salinity, transparency, dissolved oxygen in fish ponds are suitable for breeding, and ammonia nitrogen, nitrite nitrogen concentrations are also below the safe concentration.