Abstract: In this paper,the structural model was applied in Nanjing Guquan ecological engineering experimental farm to analyse and optimize for its ecosystem structure. The results obtained were as follows! 1.The experimental farm should be classified four layers. Two of four layers were composed of recycling units. 2.The orientation of energy flow must follow the order of layer distribution, otherwise, this ecosystem can not gain optimal ecolomic benifits.3.The ecolomic binifits of experimental farm will be raised distinctly while organization of production according to the optimal structure. It was estimated that the output value of the new structure will be at least 1.5 times as that of the original structure without any additional investment.