Sustainable land use system in agricultural developing zone consists of many factors such as social, economic and natural environmental factors, in which mutual effects among the factors determine the dynamic development of the system. It is the premise and basis to master the structure arrangement and mutual effects in studying sustainable land use and establishing the corresponding evaluation index system in agricultural developing zone. In this article, Jinan Agricultural Developing Zone is taken as an example. Based on the establishment of structure model for sustainable land use system in agricultural developing zone, the methods of Boolean operations and decomposing the reachable matrix are used, and in the end the structural matrix and modeling chart are worked out by means of Interpretive Structural Modeling (ISM). Furthermore, the evaluation index system framework is discussed to test the model. The result suggests that the model displays clearly the spatial step up relationship of factors in land use system, thus providing the basis for establishing evaluation index system for sustainable land use in Jinan Agricultural Developing Zone.