This paper analyses agricultural green efficiency and productivity by using the farming and livestock industries as case studies. To do so, nitrogen and phosphorus surpluses in arable land are measured by considering recycling of agricultural wastes in the farming and livestock ecosystem and defined as the undesirable output in agricultural production. The empirical analysis is based on data of rural areas in Anhui province, China, over the period of 2000 to 2017. It shows the existence of considerable nitrogen and phosphorus nutrient surplus in arable land, with phosphorus surplus keeps increasing. It also illustrates that nitrogen and phosphorus nutrients from manure were decreasing while those from the crop residues were increasing. The empirical assessment demonstrates that agricultural green efficiency tended to converge over time. Furthermore, agricultural green total factor productivity showed an overall increasing trend, although its components, efficiency change and technological progress, moved in opposite directions in most years. Finally, some useful policy recommendations are provided in this paper.