Effective flood management measures incorporate the flood mitigation functions of natural ecosystems,but the exact functions and effects of forests, grasslands and other ecosystems in mitigating floods are not clearly understood. In this paper, a flood mitigation assessment model was established based on the Soil Conservation Service (SCS) method, and the function and potential capacity of ecosystems for mitigating flooding in the Upper Yangtze River Basin (UYRB) were assessed. The monetary value of flood mitigation service was calculated by formulating an exponential function with respect to the amount of storm and flood damage. The results showed that ecosystems in the UYRB reduced flooding by a total of 42.8 billion cubic meters. Statistical equations developed for the amount of storm and flood damage gave an average of 6.479 billion RMB Yuan as the value of ecosystem flood mitigation in the UYRB. Despite their small cost, ecosystems have the potential to reduce flood damage by more than half, an indication of the important role of ecological systems in flood management. This approach can be used to identify high-value areas for ecological protection, and also to provide the governments at various levels with important information for decision-making related to integrated flood management.