Abstract: Sustainable development is a shared goal of all countries around the world. The assessment of regional sustainability is becoming an important theoretical basis for policy making. Gannan Tibetan Autonomous Prefecture is a typical alpine pastoral region in China. In this region, sustainable development has become a major issue with the ongoing development of animal husbandry. Therefore, we analyzed the sustainable development of counties and cities in Gannan from 2005 to 2013 based on a modified emergy ecological footprint model. Regional emergy densities are the key of the modified model, which was used to quantify the ecological carrying capacity and the ecological footprint. Therefore, this model can truly reflect the supply capacity of ecosystems and human resource consumption in these areas. The results indicated that livestock products accounted for the largest proportion of the ecological footprint in the study area, and remained stable during the study period. The percentage of electricity and coal consumption increased year by year, while the proportion of farming products and wild firewood decreased. The per capita ecological footprint in Gannan increased from 4.77 ha per capita in 2005 to 7.09 ha per capita in 2013. The per capita ecological carrying capacity fluctuated between 4.64 ha per capita and 5.65 ha per capita. The ecological footprint index of Gannan showed a decreasing trend, and its ecological environment had an unsustainable development status during the study period. The ecological footprint per ten thousand yuan GDP in Gannan dropped from 12.60 ha per ten thousand yuan in 2005 to 4.86 ha per ten thousand yuan in 2013, revealing that the resource utilization efficiency had improved. Among the counties and cities, Hezuo had the highest ecological footprint index, followed by Diebu. There were no significant differences among the other counties. In general, the per capita ecological footprint and ecological carrying capacity were higher in regions of animal husbandry development (Maqu, Luqu, Xiahe, and Hezuo) than in regions with a farming-pastoral ecotone (Lintan, Zhuoni, Zhouqu, and Diebu). During the 9 years, Diebu, Maqu, and Luqu had a sustainable development status while Xiahe, Zhuoni and Zhouqu had an unsustainable development status. Hezuo and Lintan had a seriously unsustainable development status. Based on these findings, we discuss the future sustainable development of Gannan.