Soil nutrients loss is the main way of non point pollution from farmland. Taking a typical small watershed of three gorges area as an example, this paper considered the soil nutrients loss character and the predicted amount of soil loss of a pixel, and introduced a nutrient prediction equation.Integrated GIS and the equation, amount of nutrients loss were predicted. The results showed that organic matter, total nitrogen, phosphorus and potassium average annual loss are respectively 30.5, 2.8, 0.9, 68.1 t/km 2. Using average amount of fertilizer application and organic matter accumulate rate to judge nutrients loss risk degree, we found that most nutrients losses are serious in the watershed. The its amount is over half of fertilizer application.