Global climate change and air pollution pose severe challenges to human survival and development. Pollutants and greenhouse gas (GHGs) emissions can change atmospheric chemical composition and climate . To prevent an ecological crisis and ensure the harmonious coexistence of man and nature, China has proposed a vital national strategy of forging an Ecological Civilisation (EC) in the country based on socialistic principles. The agricultural sector is one of the main sources of air pollution and GHG emissions. There exists a lack of systematic research on the emission characteristics, their future paths, as well as control strategies; this hinders the coordinated responses to GHG emissions and air pollution that could otherwise lead to an improvement in the situation. By creating an emissions inventory of homologous atmospheric pollutants and GHG of similar origins in China’s agricultural sector, we analysed the drivers through the Logarithmic Mean Divisia Index (LMDI) model. We predicted the future path based on the measured emission reduction potential. The research results show that agricultural production and GHG emissions have been steadily decoupled, with macro-control by the government being the most important driving factor in keeping emissions under control. A nature-based action plan for the coordinated control of GHGs and air pollutants in China based on eco-agriculture can result in the harmonious coexistence between man and nature in the future, by realising a socialist EC and agricultural carbon neutrality simultaneously by the middle of the 21st century.