China’s agriculture is dominated by smallholder farms, which have become major sources of negative environmental impacts including eutrophication, formation of haze, soil acidification, and greenhouse gas emissions. To mitigate these environmental impacts, new farming models including family farming, cooperation farming and industrial farming have emerged in recent years. However, whether these new farming practices would improve the economic and environmental performance as compared to the current smallholder farming has yet to be verified on ground level. In this paper, by using pilot farming cases within the watershed of Tai Lake, we found that alternative farming models produced 7% more crop yield, while using 8% less fertilizer, leading to an 28% decrease in pollutant emission per hectare. These alternative farming models have a 17% higher fertilizer use efficiency and 50% higher profit per hectare. Compared to smallholder farming, these alternative farming practices invest 27% more resources into agricultural facilities, including advanced machinery, and have a younger, better educated labor force as a consequence of a larger farm size and more specialization. These input changes substantially increase fertilizer use efficiency and reduce agricultural pollution. Policy arrangements to support and facilitate the uptake of these farming models will further promote the green development and sustainable intensification of agricultural production.