This paper analyze the characteristics, composition of coal enterprises' logistics center in detail. The key factors that affect the logistics cost control are found from internal and external aspects. Causal relationship of logistics cost system is established in logistics center. Then, structure model of enterprises' logistics cost system are built with different impact factors. The model indicated that the complex relationship among factors of enterprises' logistics operational cost system could be better revealed the key links between logistics center and the cost control, and the model proposed can guide coal enterprises' logistics cost control.