Since there are the facts of the multi-level, multi-objective and fuzziness in water resource allocation decision of inter-basin water transfer project, according to multi-objective fuzzy optimization theory, an appropriate evaluation index system of regulation and storage scheme was established. Meanwhile, considering the multi-management of inter-basin water transfer project, decision-maker weight was introduced on the basis of original weight calculation. A multi-objective fuzzy optimization model is established, consequently providing group relative optimal degree with comprehensive evaluation. The method is applied in analysis and optimization of Jialingjiang-to-Hanjiang River Water Transfer Project, thus the optimal scheme is acquired. The results obtained show that the model has strong applicability and flexibility，which provides a scientific method for scheme decision. It supplies decision support in demonstrating the project's feasibility and plays an important role in accelerating the balanced allocation of regional water resources.