Water resource assessment based on the hydrological model provide scientific basis for solving the problem of water shortage and improving the mode of water resources management and utilization. In this study, the SWAT was used in the assessment of water resources, and analyze the spatial and temporal distributions of blue and green water resources in the Wuyuer River Basin. The results show that the green water resources occupying the large proportion in the total water resources, and play an important role in sustaining the water security, food security and stability of ecosystem. The innovation which brings the green water resources into traditional water resources assessment is imperative.