The agricultural resources of Xiannangou watershed were not used efficiently, the system of agricultural practices grow inconsistently with agricultural resources, and the chain network structure of ecological agricultural system with commodity(EASC) was incomplete. In order to solve these problems, Three phases and five scenarios of the possible development path of ecological agriculture with commodity(EAC) was set on the principle of clean development mechanism(CDM), and further efforts were made to optimize the EASC. The results showed that the economic benefits of each phase had been improved and the land use structure had also been significantly changed after the optimized of EASC. The economic benefits of phase Ⅰ to Ⅲ had been improved by 34.4%, 53.0~55.2%, and 72.8~73.7%, respectively comparing with the actual state. On the principle of CDM, the coupling of agricultural economic system and agricultural ecosystem, a better land use structure(agriculture:forestry:animal husbandry=1:12.6:4.4) was produced, implying that the proportion of forestry increased compared to phase Ⅰ and phase Ⅱ.The development progress of EASC with the development trend of the actual state→the modified chain network construction of EASC→the optimization of agricultural economic system and agricultural ecosystem coupling has its historical inevitability.