Today's organizations face a complex set of needs of their stakeholders. They cannot satisfy those needs in a good manner because of economical rationality or inability to prepare suitable equipments. So inter-organizational relationships have been choosen as a strategy which nowadays attract much attention. In fact, each organization has a set of interorganizational relationships voluntarily or involuntarily with other organizations which many organizational advantages and disadvantages have roots in such a inter-organizational relationships. Therefore, the Present research aimed at developing a simulation based model to study inter-organizational relationships. In this model, inter-organizational relationships are documented with process approach, and then. analyzed based on volume, time, human recourses, mutual dependency network and decision. According to the analysis results, "to-be" process is redesigned. These changes are suitability analyzed with simulation and implemented if they are confirmed. Finally this model has been implemented in Agriculture Industry Bureau of Jihad -Agriculture Ministry.