[Objective] The probability of flood occurrence and its risk distribution in Lijiang River watershed were mapped to provide some references for regional flood risk assessment from the aspects of watershed eco-hydrological function.[Methods] The maximum and minimum water holding capacities in surface soil(0-10 cm) and annual rainfall were analyzed using geostatistics and spatial overlay analysis.[Results] The surface soil drain ability(difference between maximum and minimum water holding capacity) and annual rainfall displayed a strong spatial autocorrelation(spatial autocorrelation coefficient > 0.88). But the spatial autocorrelation of surface soil drain ability was controlled by random factors rather than by autocorrelation factors, which resulted to its lower spatial structure in comparison with the one of annual rainfall. The tri-junction area of Guilin urban area, New Lingui District and Lingchuan County has the highest risk of flooding; whereas three nature conservation areas, namely Maoershan National Nature Reserve, Haiyangshan and Qingshitan Water Conservation areas have the lowest risk of flooding.[Conclusion] Considering both the eco-hydrological function of watershed and climate change(mainly referred to rainfall) in this study, we can predict the probability of flood occurrence and map the flood risk distribution in Lijiang River watershed. The junction are of Guilin urban area and Lingchuan County is the flood-prone region. This study hopes to provide a scientific knowledge for regional flood disaster prediction and evaluation, also for prevention and mitigation of flood disaster.