Fertilizer is one of the important commodities in Indonesia on farming productivity. In 2001, Indonesia’s government transformed the fertilizer’s industry from a regulated industry to an open industry that caused the misleading of fertilizer’s distribution and pricing. The latest policy in 2006 contained the guiding principle for procurement and distribution and the amount of subsidy of fertilizer commodity for each appointed manufacturer. The arrangement process of work regions is called regionalization and the amount of subsidy is called subsidized cost.We purpose an integrated model of regionalization which adapts characteristics of fertilizer’s procurement and distribution (distribution pattern, demand fluctuation) to organize the responsibility area of fertilizer’s manufacturer and a subsidized cost model that will result the optimal amount of cost subsidy from government to the manufacturers to guarantee the same fertilizer’s maximum pricing until its end user. The references models are from Nur Bahagia and Sofitra (2001), which have developed an optimization model for single manufacturer, single warehouse, and multi retailers and Vidal and Goetschalckx (2001), which have developed a global supply chain model with transfer pricing and transportation cost allocation. The logistics total cost will become the performance criteria for this developed model. Solution for this model uses MILP.