The paper has analyzed present aquiculture conditions and controlling problems of water environment factors of aquiculture, and constructed effective security aquiculture breeding intelligence controlling system suitable to Chinese situation, and presented the control strategy of neural network realizing dynamic decoupling for the factory aquiculture, and specially solved the water environment control and so on the key questions. The long term practice has shown that the system operation is simple and effective safe by applying some breeding bases in Zhenjiang, the system has met the requirements of culturists and enhanced international market competition for aquiculture.