Ecological footprint is a biologically productive land that can produce the materials needed to meet the productive needs of human life and absorb the waste generated by humans in the region. Ecological footprint evaluation system can describe the impact of regional social and economic development on local ecological environment to a certain extent, but one of the difficulties in current sustainable development research is how to more truly reflect such impact. Based on traditionally ecological footprint model, this study firstly calculates the equilibrium factor and yield factor by year and by subregion. We improved the construction land footprint algorithm through combining the land use transfer matrix. Finally measured the ecological footprint and ecological carrying capacity of Northern Xinjiang in 2005, 2010, 2015 and 2018, and evaluated the sustainability of development in the study area. The results showed that:(1) the ecological footprint of the Northern Xinjiang increased by 3.5 times, which was dominated by energy footprint, while the contribution of biological productivity footprint decreased significantly. Per capita ecological footprint increased by 3.4 times, and the growth rate of ecological footprint and per capita ecological footprint of industrial cities were both higher than other types of cities. (2) The ecological carrying capacity of the study area showed an upward trend except for water and grassland. The overall and per capita carrying capacity of Changji and Altay were both declining. (3) The ecological efficiency of Northern Xinjiang increased by 1.32 times. The units showed a trend of increasing ecological efficiency in agricultural and service-oriented cities and decreasing in industrial cities, indicated that the growth rate of ecological footprint of industrial cities was higher than the corresponding cities' economy. (4) The ecological deficit of each unit was increased, and the growth rate of overall and per capita showed a trend of industrial cities > agricultural cities > service-oriented cities. Overall, ecosystem security in the study area was at an average level, and the ecological system and economic system were in a coupling state. But there was a risk of security decline caused by the surge of ecological footprint. Some cities were in a low coupling or even decoupling state, and the overall sustainability was reduced. Therefore, in the future development process, government should combine national and regional policy guidance with our own geographic and resource advantages, actively optimize the industrial structure, improve the efficiency of resource utilization, to build a diversified, healthy and sustainable new development system.