Floodarea is a joint product of Geomer GmbH, Heidelberg, Germany. It is a 2 D dynamic flood evolution model, established based on GIS raster. In order to study the evaluation method of risk precipitation in small valley of mountain areas, a case study was performed for Shangqing River Valley, which lies in Fujian Province. Hourly area precipitation of the valley is calculated by using Thiessen polygon method of GIS and according to the rainy days of meteorological observing station. Coefficient of runoff formation and surface hydraulic power roughness is calculated with GIS on the basis of landscape in the valley. Based on precipitation data and digital elevation model data of 1:10000, the flood process which happened on June 18, 2010 is simulated with the “Floodarea” model. The water depth and water velocity is adjusted by means of changing coefficient of runoff formation and surface hydraulic power roughness, according to the differences between actual water depth and simulated water depth. The results show that tested by the research data after the flood process, the maximum water depth and its time are simulated well for the Shangqing River Valley. So the risk precipitation of different water depth grades in the valley can be calculated according to the simulated data.