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In this paper, an inventory control model is build by using colored Petri net. In order to verify the colored Petri net model, it is simulated by using the data of a company. The simulation result shows that it is coincident with the empirical data. By using the model, the relationship of stock and shortage rate is analyzed. It is found that when interval of customer order received is random, the safe stock and shortage rate do not fit the theory of general inventory control.