Sustainable alternative farming systems are gaining popularity worldwide because of the negative effects of conventional agriculture on global climate change and the environmental degradation caused by intensive use of synthetic inputs. The green farming system in China is an integrated production strategy that focuses on reducing chemical fertilizer use while increasing organic manure inputs. Despite their rapid growth as more sustainable systems over the past decades, green farming systems have not been systematically evaluated to date. We used apple production as a representative case to assess the sustainability of green farming systems. Across major apple-producing regions in China, green farming reduced the application of chemical fertilizer nitrogen (N) by 46.8% (from 412 to 219 kg ha−1) and increased that of manure N by 33.1% (from 171 to 227 kg ha−1) on average compared with conventional systems enhancing N use efficiency by 7.27–20.27% and reducing N losses by 8.92%–11.56%. It also slightly lowered yield by 4.34%–13.8% in four provinces. Soil fertility was improved in green orchards through increases in soil organic matter, total N, and available major nutrients. Our cradle-to-farm-gate life-cycle assessment revealed that green farming helped to mitigate greenhouse gas emissions by an average of 12.6%, potentially contributing to a reduction of 165 239 t CO2 eq annually in major apple-producing areas. In addition, green farming achieved 39.3% higher profitability ($7180 ha−1 year−1) at the farmer level. Our study demonstrates the potential of green production of apples for the development of sustainable agriculture in China. These findings advance our understanding of sustainable alternative farming systems and offer perspectives for the sustainable development of global agriculture.