The chapter is devoted to modeling and analysis of supply systems. Supply chain management is more and more affected by network and dynamic business environment. In supply chain behavior there are inefficiencies. Coordination and cooperation can significantly improve the efficiency of supply networks. There are some approaches to model and analyze the supply dynamics. Important features of this environment are established in the proposed approach. The combination of network structure modeling and simulation of dynamic behavior of units in supply network can be a powerful instrument of performance analysis of supply networks. The problem of coordination in dynamic supply networks involves multiple units with multiple goals. Multicriteria analysis of supply network performance includes such criteria as quantity, quality, time, cost, and profit. Simulation approach is an appropriate tool for prediction of real supply situation.