Improving China’s agricultural greenhouse gases (GHG) emission efficiency has become an important way to cope with climate change in an ecologically—and ethically responsible manner. In this paper, we use a global slacks-based inefficiency model to evaluate the agricultural greenhouse gases (GHG) emission efficiency levels in China during 2000–2015. The regional disparity of China’s GHG emission efficiency is examined by using a Dagum Gini coefficient. A spatial Markov chain technique is also employed to investigate the spatial dynamic evolution of agricultural GHG emission efficiency. The results show that: (1) China’s agricultural GHG emission efficiency increased steadily during the study period; a certain gap in efficiency among provinces and regions also exists. (2) Between-group disparity is the main source of the overall regional disparities in China’s agricultural GHG emission efficiency. The disparities between regions are on the rise, while the disparities within regions are relatively stable. (3) China’s agricultural GHG emission efficiency demonstrates significant spatial dependence. This study provides policy implications for the sustainable development of China’s agricultural sector.