Soil erosion is a significant factor in the deterioration of the ecological environment and soil conservation is an important ecological service of National Key Ecological Function Areas in China. Here, climate, terrain, soil and vegetation cover, soil erosion and soil conservation spatial data in 25 National Key Ecological Function Areas in 2010 were analyzed using the Universal Soil Loss Equation by ArcGIS tool. We found that soil conservation effects due to vegetation cover and soil conservation measures are obvious and that micro and slight erosion areas in National Key Ecological Function Areas have increased by 26.2%. The area of intensive erosion decreased by 25.1%, and the soil conservation amount in southern National Key Ecological Function Areas is high. The conservation amount of soil nutrients within National Key Ecological Function Areas is related to amount of soil conservation and content of each nutrient element in soil. The sequence of nutrient conservation amounts from high to low is soil organic carbon, total K, total N and total P in soil. The conservation amount of various soil nutrient elements in the Alkin Grassland function area and Yunnan and Sichuan function area was highest. Based on our findings, we recommend the strengthening of vegetation protection and management in the areas with high per unit area soil erosion, enhancement of vegetation cover and improvement of soil conservation measures in order to improve soil conservation functions and reduce soil nutrient losses. Vegetation protection and soil conservation measures should be consolidated in the areas with high potential erosion to prevent further deterioration.