Abstract: The Central Document No.1 in 2019 has put forward the action plan for the development of green agriculture. As an important aspect of green agriculture, the development of low-carbon agriculture is an essential measure. How to accurately measure the efficiency of the low-carbon agricultural development and analyze the law of evolution is of great significance to accelerate the development of low-carbon agriculture. By taking the agricultural inputs, paddy fields, livestock and poultry breeding, and energy consumption as the carbon sources, the agricultural carbon sink was introduced as the desirable output from the perspective of low carbon. Then, based on the metafrontier method combined with the global Malmquist model, the low-carbon agricultural development efficiency of 30 provinces (districts, cities) in China from 2000 to 2016 was calculated, and the efficiency was further decomposed to identify the sources and rules of efficiency growth. The results showed that the overall efficiency of the low-carbon agricultural development in China showed a significant upward trend. By region, the eastern region has taken the leading position, the western region has remained stable, and the central region has been catching up. By province, the low-carbon agricultural development level in Beijing had absolute advantage, while Jiangxi Province had the lowest. From the perspective of growth sources, the improvement for the efficiency of low-carbon agricultural development mainly depended on the growth of agricultural technical progress, but the agricultural technical efficiency has been in a state of deterioration at present. Therefore, China should adopt the following measures such as combining the characteristics of regional resources, breaking the regional restrictions of provinces and increasing the exchanges of agricultural production, thus to improve the efficiency of low-carbon agricultural development and promote the realization of low-carbon agriculture.