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Whether an enterprise is able to survive during the cruel competition or not is mostly dependent on the cost of investment. Enterprise resource planning (ERP) has been adopting by more and more enterprises and acquires comprehensive admit because it brings out great benefit for the enterprises. A framework of the system coupled by the cost management of ERP is designed. How to design a rough and artificial neutral network is analyzed based on the theory of rough sets with some reduction. The model based rough sets neural network prediction is more efficient and higher precision than BP model in cost prediction.