With the development of modern logistics system, the automatic logistics distribution centers have been built in most tobacco enterprises. The packaging system plays important role in the distribution center, it is necessary to construct a set of scientific method to evaluate the packaging system mode. According to the real situation of tobacco logistics distribution center, the cost and benefit are set to the general goal. For these three modes of packaging system, packaging by hand, automatic packaging and packaging by heat-shrinkable material, the evaluation index system and hierarchical structure are built. Refer to the hierarchical chart and the principle of AHP, the weight of each index is calculated. On the basis of weight that worked out by AHP, the final evaluation result can be found and analyzed follow the principle of fuzzy comprehensive evaluation. Finally, reference the consequences of the FCE, the DEA model based on FCE is used to enhance the integrality and systematic of the evaluate result.