In the past few decades, a series of ecological restoration and protection projects had been implemented in the Inner Mongolia region. However, which extent these projects met the satisfaction? In this paper, from the perspective of land use/land cover data and DPSIR conceptual framework, we systematically describe spatial and temporal changes of ecosystem services values and analyze driving factors of these changes from both the regional and the prefecture-level scale, adopting the parameters of the stock value, intensity of the stock value and the incremental value. The results show that:(l) Since 2000, the whole region's stock value had increased by only 0.24%, but the decreasing rate of the cumulative positive and negative incremental values had promoted by 32.9%. There are more changes occurred in the eastern area than in the western area; (2) Since 2000, after the "Grain for Green" policy was carried out, the stock values of ecosystem services in the plain cultivation areas and forests conservation areas had increased by 4.52% and 4.23% respectively, yet the incremental values had increased by 0.59 billion and 0.89 billion respectively. All the changes was constrained by climate change, population growth and a series of political and economic macro-policies; (3) Since 2000, the stock value had increased by 3.51%, while the incremental value still decreased by 0.42 billion in the highland steppe areas, which was constrained by the precipitation fluctuations and population growth factors; (4) Since 2000, the positive influences of human activities in central and eastern areas gradually increased from 45.8% to 76%; however, under the traditional way of economic development, the ecological protection in the midwest areas still faced great difficulties and pressures. The result of our study provides a scientific reference for dividing eco-zone and constructing eco-restoration, and it could be further utilized in establishing a suitable ecological compensation mechanism.