The Hulunbuir region of Inner Mongolia, China, was chosen as the study area of the current study. The super-efficiency DEA (Data Development Analysis) model and Malmquist index were combined to examine the spatial and temporal changes in ecological efficiency in the counties in the Hulunbuir region. Ecological efficiency in the Hulunbuir region was low in 2000 and increased in 2000——2015 in each county, with no obvious advantage in any particular county. Among the counties, ecological efficiency was relatively high in Yakeshi (1.59), Hailar (0.96), and Morin Dawa (0.90) and relatively low in Chenbarhu (0.57) and Xin Barag Right Banner (0.67), and there was a substantial increase in Morin Dawa from 0.09 in 2001 to 0.90 in 2015. Based on the Malmquist index, technology was the main driving factor for the improvement in ecological efficiency and also the main factor that restricts the development of grassland and animal husbandry. Additionally, policy factors, climate change, and production input factors had a substantial influence on ecological efficiency. Therefore, increasing investment in science and technology and large-scale operations are deemed to be of great importance for improving ecological efficiency. It is necessary to intensify the protection of grassland areas, draw red for ecological protection, and improve the system of compensation to promote the sustainable development of these prairies.