The response of natural vegetation to climate change is of global concern. In this research, changes in the spatial pattern of major terrestrial ecosystems from 1956 to 2006 in Inner Mongolia of China were analyzed with the Holdridge Life Zone (HLZ) model in a GIS environment, and net primary production (NPP) of natural vegetation was evaluated with the Synthetic model, to determine the effect of climate change on the ecosystem. The results showed that climate warming and drying strongly influenced ecosystems. Decreased precipitation and the subsequent increase in temperature and potential evapotranspiration caused a severe water deficiency, and hence decreased ecosystem productivity. Climate change also influenced the spatial distribution of HLZs. In particular, new HLZs began to appear, such as Warm temperate desert scrub in 1981 and Warm temperate thorn steppe in 2001. The relative area of desert (Cool temperate desert scrub, Warm temperate thorn steppe, Warm temperate desert scrub, Cool temperate desert and Warm temperate desert) increased by 50.2% over the last half century, whereas the relative area of forest (Boreal moist forest and Cool moist forest) decreased by 36.5%. Furthermore, the area of Cool temperate steppe has continuously decreased at a rate of 5.7% per decade; if the current rate of decrease continues, this HLZ could disappear in 173 years. The HLZs had a large shift range with the mean center of the relative life zones of desert shifting northeast, resulting a decrease in the steppe and forest area and an increase in the desert area. In general, a strong effect of climate change on ecosystems was indicated. Therefore, the important role of climate change must be integrated into rehabilitation strategies of ecosystem degradation of Inner Mongolia.