Ecological sensitivity refers to the reflection degree of the ecosystem to human activities and natural environment's changes; it explains the accessibility and possibility of the effect of regional ecological environment. Watershed ecological sensitivity is the degree of difficulty and possibility of ecological imbalance and environmental problems when the ecosystem encountered interference. Biodiversity is the most important ecological factor that can be affected by the Watershed ecological sensitivity. By considering the main biodiversity sensitive factors such as ecosystem types, species richness, rarity, endangered and protected level, this paper identified the ecological effects possibility of watershed dam and reservoir projects. By means of GIS technology's powerful and spatial data acquisition, processing and modeling analysis capabilities, the biodiversity sensitivity index was calculated based on the weights of the expert's score. Sensitivity partition was achieved in accordance with the principle of ARCGIS natural breaks methodology based on the secondary basin area maximum integrated sensitivity index. The results show that the most sensitive areas are mainly located at Min Tuo Jiang, Jinsha river Shigu downstream, Jinsha river Shigu upstream, Yibin to Yichang and Jialing River of Yangtze River region; Yujiang, Hongliuhe and Xijiang of Pearl River region; Lancang River, Red River, Nujiang and Irrawaddy River of Southwestern rivers region; Longyangxia's upstream of Yellow River region. These areas which have rich kinds of endemic aquatic species, threatened species and intensive national nature reserve, are the most abundant biodiversity areas. Insensitive areas are mainly at Songhua river region except the second Songhua river area, Tarim basin desert, Gurbantunggut desert, central & western Asian inland river and Mainstream of the Tarim River in Northwestern rivers region. The characteristics of Songhua river region are low temperature, forestclimate steppe climate, wet, big farmland and waters climate, and the engineering reservoirs are less likely to affect biodiversity. The desert areas in the Northwestern rivers region have harsh ecological and poor biodiversity enviroment, also an insufficient condition of building a large reservoir with a low biodiversity sensitivity.The sensitivity of other areas is between the two areas that mentioned above, different sensitivity of biodiversity depends on its ecosystem types, species richness, rarity, endangered and protected level. The main area in Songhua river region is insensitive area, which occupies 91.92% of total area. Liaohe area is mainly less sensitive area and sensitive area, the percentages are 52.83% and 47.17% respectively. The main area of Yellow river region is sensitive area, and Longyangxia to Lanzhou is more sensitive area. The main area of Yangtze River region and Pearl River region is the most sensitive area, the proportion percentage is 50.47% and 50.46% respectively. The more sensitive area of southeastern rivers region is 70.70% of the whole area. The most sensitive area in Southwestrn rivers has 46.57% of the Southwestern rivers area, and the sensitive area in Southwestern rivers is 53.43%. Qinghai Lake river system of the Northwestern rivers region is more sensitive area, the oasis on the edge of the desert and the piedmont area is sensitive area. It can be used to provide a scientific prove of reasonable and suitable development for the river water resource in the future by recognizing the biodiversity's susceptibility causing by reservoir engineering.