Taking Qinzhuanggou watershed in dry upland of northern Weihe River as a case, the interactive relationship of ecology, economy and society in small watershed system was analyzed. Using VENSIM software to build a dynamic model of SEE(society-ecology-economy), with focusing on soil and water conservation, taking the methane pool as link, the goal of management of ecological subsystem, economic subsystem and social subsystem as the judgment basis, and quantitatively analyzing the comprehensive governance efficiency of ecological subsystem, economic subsystem and social subsystem. Moreover, the simulation of the development trend from 2011 to 2026 was made by using the dynamic model of SEE. The result showed that the 3rd scheme(subsistence mode that the per capita grain yield goals is 350 kg) can be taken as the optimization scheme for soil and water conservation and ecological design, the declining trend of Qinzhuanggou watershed system will be changed, such as water and soil loss will be controlled effectively, point and non-point source pollution will be eliminated, ecological agriculture will be developed, income per capita will be RMB 6 000 yuan, rural drinking water safety will be realized fully, the trip will be convenience, living environment will be improved.