From the perspective of green operations, establishing an indicator system of multiobjective shipping arrangement which took into account the technical, economic, environmental and other factors, gave the judgment matrix of advanced technology, economic rationality, Environmental coordination and target layer consistency by using the method of Fuzzy Analytic Hierarchy Process. According to the fuzzy consistent judgment matrix, calculated the relative importance weights coefficient of each index of the criterion layer with respect to the target layer. According to multi-route and multi-boat liner shipping problems to establish mathematical model of multi-objective shipping route arrangement .For the multiple variables and multiple constraints problems of this model to give Ant Colony Optimization Model that suitable for liner shipping, and finally by comparing example with single-objective shipping arrangement and existing scheduling mode demonstrated the effectiveness of the proposed method, providing a new way for green operations.