Ecological security is the basis and premise to ensure the sustainable development of human society and economy. Evaluating the temporal and spatial evolution and influencing factors of ecological security is of great significance to its ecological security pattern construction and regional sustainable development. Based on the localized ecological footprint model, we calculated the ecological footprint, ecological surplus and deficit and ecological stress index of twelve cities across the Inner Mongolia in China from 1990 to 2018. Entropy method was conducted to construct a comprehensive index system, calculating the ecological safety index, and evaluating the state of regional ecological safety and sustainable development. We also combined spatial analysis to reveal its temporal and spatial evolution and analyze the driving factors of temporal and spatial dynamic. The results showed that (1) during the study period, the Inner Mongolia was in a state of ecological deficit, but the growth rate of ecological carrying capacity was greater than that of ecological footprint. In 2018, the per capita ecological footprint and per capita ecological carrying capacity increased by 0.9-5.8 times and 1.5-10.8 times respectively compared with 1990. The ecological safety index changed from an unsafe state to a safe state, and the value changed from over 5.0 to less than 4.0. The ecological station of whole study area improved. (2) The spatial distribution of ecological footprint indicated a "high in the east and low in the west" situation across the Inner Mongolia. However, the spatial variation of ecological carrying capacity indicated a "high in the middle and low in the two wings" spatial distribution. During the study period, the ecological security center of the study area shifted to the northeast. (3) The economic level, consumption expenditure, and industrial structure are the driving factors for ecological security and sustainable development in the Inner Mongolia. Moreover, geographical location and climate factors are the leading factors for its spatial differences.