High-quality development has become a new requirement for China’s social and economic development. As an important industry related to the national economy and people’s livelihood, achieving high-quality development in agriculture has become the most urgent task currently facing agriculture. This study focuses on agricultural eco-efficiency to indicate spatial distribution of high-quality development based on agricultural input–output data from 2001 to 2019 and the SBM-Undesired model; this study focuses on Agricultural Eco-efficiency, a key indicator related to the high-quality development of agriculture, to measure the temporal and spatial evolution of Agricultural Eco-efficiency. The results show that the Agricultural Eco-efficiency has increased from 0.363 in 2001 to 0.818 in 2019, with a growth rate of 125.34%, and the provinces with higher agricultural eco-efficiency are mainly located in the eastern regions. In addition, there is a U-shaped change trend between Agricultural Eco-efficiency and the total output value of agriculture, forestry, animal husbandry, and fishery. In other words, the provinces with the total output value of agriculture, forestry, animal husbandry, and fishery in the low range and high range enjoy higher Agricultural Eco-efficiency. Compared with the eastern region, the middle reaches of Yellow River and middle reaches of Yangtze River have great potential to reduce carbon emissions. In order to achieve high-quality agricultural development, it is necessary to pay attention to key indicators for improving Agricultural Eco-efficiency, and the technology development of the central and western regions will be very useful to decrease the gap.

The research on agricultural eco-efficiency has become an important point to deeply understand the interaction between ecological and environmental conditions and socio-economic factors as well as realize the coordinated development of agricultural economic development and environmental protection. (1) Background: This paper attempts to provide scientific support for the healthy and stable development of the agricultural economy and the sustainable development of ecological agriculture. (2) Methods: From a comprehensive perspective, this paper systematically analyze the overall situation, development trend, key fields, and hot fields of agricultural eco-efficiency in the past two decades. It consists of two complementary parts, including systematic quantitative literature review (based on CiteSpace) and traditional literature review. (3) Results: Agricultural eco-efficiency has evolved significantly with the popularization of agricultural machinery and the wide application of science and technology in the field of agricultural ecology. Its future development relies on the advances in our knowledge on theories and hypothesis, evaluation methods, impact on “socio-economic ecological” system, and drivers and regulation of agricultural eco-efficiency. For each of these fields, we find that challenges still exist. At present, the quantitative methods and index selection are not unified. We should deeply analyze the internal and external driving force of the development and change of ecological efficiency by constructing a complete theoretical framework for the research of agricultural ecological efficiency. At the same time, new technologies and methods are needed to evaluate agricultural eco-efficiency, and a balanced consensus between the improvement of agricultural eco-efficiency and the improvement of the ecological environment should be formed through empirical research.