Abstract: The supply chain of a virtual enterprise is dynamic alliance formed from different types of enterprises in order to attain some objective. It is task oriented, has uncertainty and goes after high efficiency. So that it is required that analyzed model of the supply chain system of virtual enterprise should have more flexible structure to fit frequent changes in generic situation. A model of the unified supply chain system based on color and stochastic Petri net is presented. Any supply chain system is described abstractly as a color stochastic Petri net that has the same structure in the model, and a certain supply chain is determined by the initial mark and the route time delay function in the model. Making use of the process simulation of production and transportation, operational status of the supply chain system is analyzed with given structure and speed of supply goods. The model is decomposed further, and the performance of the supply chain model is calculated by using isomorphic Markov chain. Complexity of calculation is avoided that is due to status explosion. An example through out the paper illustrates how the supply chain system is affected by its structure and speed according to analysis qualitatively and quantitatively.