Analyses of desertified land and land use change in Naiman County of Inner-Mongolia showed that there was a fluctuated increase of rain-fed cropland in the period from 1951 to 1960, then decreased until the middle of the 1990’s, then increased again, while irrigated cropland consistently increased. The woodland and build-up land consistently increased while grassland area decreased. The area of water body increased from 1975 to 1995 and then decreased while river beach decreased. Wetland change fluctuated with a maximum of 303.53 km2 in 1995 and a minimum of 62.08 km2 in 2002. Invasion of cropland into river beach does not only change land coverage on the beach, but also the hydrological process of the river systems and deeply influence water availability. The correlation between cropland and underground water table is negative and significant. Increase of irrigated cropland is the primary cause of water availability reduction. Water table reduction is negatively correlated to cropland. The total desertified land has decreased since 1975. A rapid increase occurred before 1959, but it is difficult to assess the change of desertification due to lack of data from 1959 to 1975. Changes of different types of desertified lands were different. There is no significant correlation between land use and different types of desertified land, but there is a significant negative correlation between woodland and total desertified land. The correlation between grassland and total desertified land is positive and significant. There is a significant correlation between different land cover and key factors such as water body and annual precipitation, river beach and runoff, area of shifting dune and annual precipitation, and cropland and underground water table. Desertification reversion in Naiman County is fragile and will be even much more fragile due to population growth, rapid land use and climate change. This will lead to continued invasion of irrigated cropland into more fragile ecosystems and reduction of water availability.