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The eco-port is the future development and tendency of port. Based on the composition analysis of traditional port logistics operation system, this paper introduces eco-environmental factors, constructs the evaluation index system of eco-port logistics operation system and decides the weight of indexes by using AHP. Then we acquire the score of the eco-port logistics operation system by using the fuzzy evaluation method to evaluate the advantages and disadvantages of the port logistics operation system, and further discuss the ecology features. Finally, we use a practical example to prove the feasibility of the method and offer the decision basis for the port sectors to improve the logistics operation system.