The sandstorm in 2021 in East Asia demonstrated the ecological issues that culminated for decades in Mongolia. Mongolia is facing challenges to realize green and sustainable development. This article aims to increase the understanding of eco-efficiency and its influencing factors in Mongolia and to provide a reference for similar developing countries and regions to achieve green and sustainable development. This article used the Slacks-Based Measure of Efficiency (SBM) model with advantages of dimension freedom and unit variable to estimate the economic efficiency and eco-efficiency of 22 provinces in Mongolia from 2007 to 2016; energy consumption and undesirable environmental outputs were taken as ecological/environmental indicators in the input and output system of regional eco-efficiency in Mongolia, combining traditional indicators of economic efficiency to build Mongolia’s eco-efficiency input–output framework. This article applied hot spot analysis and gravity center analysis to reveal the temporal and spatial evolution characters of eco-efficiency in Mongolia. Finally, the article applied panel Tobit regression to analyze the influencing factors of eco-efficiency. We were found that Mongolia’s eco-efficiency slightly improved from 0.7379 in 2007 to 0.7673 in 2016, lower than the economic efficiency. The high eco-efficiency provinces appeared in the capital Ulaanbaatar and its surrounding areas, showing an obvious spatial spillover effect. The low eco-efficiency provinces were mainly in the undeveloped western region. The relationship between per capita GDP and eco-efficiency was U-shaped and consistent with environmental Kuznets theory. Accelerating economic growth, optimizing population distribution, and improving energy structure and green technology can improve Mongolia’s eco-efficiency.