Cropland fragmentation contributes to low productivity and high abandonment risk. Using spatial statistics on a detailed land use map, we show that 10% of Chinese croplands have no potential to be consolidated for large-scale farming (>10 ha) owing to spatial constraints. These fragmented croplands contribute only 8% of total crop production while using 15% of nitrogen fertilizers, leading to 12% of fertilizer loss in China. Optimizing the cropping structure of fragmented croplands to meet animal food demand in China can increase animal food supply by 19%, equivalent to increasing cropland proportionally. This crop-switching approach would lead to a 10% and 101% reduction in nitrogen and greenhouse gas emissions, respectively, resulting in a net benefit of US$ 7 billion yr⁻¹. If these fragmented croplands were relocated to generate large-scale farming units, livestock, vegetable and fruit production would be increased by 8%, 3% and 14%, respectively, and reactive nitrogen and greenhouse gas emissions would be reduced by 16% and 5%, respectively, resulting in a net benefit of US$ 44 billion yr⁻¹. Both solutions could be used to achieve synergies between food security, economic benefits and environmental protection through increased agricultural productivity, without expanding the overall cropland area.