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.