Abstract: The Preference of ship owner have great influence on transit port selection. However, the published studies on transit port evaluation tend to focus on features of ports only, seldom involving the Preference of Ship owner. An assessment index system involving both port features and preference of ship owner is built. A fuzzy comprehensive decision-making strategy based on integration of AHP and evidence fusion theory is developed to deal with the differences between different specialist opinions from questionnaire. The AHP is used to decide the weights of assessment indexes and the fuzzy mathematics is used to process questionnaire feedback from experts and define the degree of membership of the measurements of indexes and the basic probability function of the opinions from experts. Evidences from experts are fused with discount evidence theory. The weighted average function is used to decide the final result according to the principle of maximizing membership function. Xiamen Port and Gaoxiong port are evaluated, which shows that both of them are at the level of "Important" as for ship owner’s preference is considered.