Objectives The middle and lower reaches of the Yangtze river are important rice–wheat rotation areas in China, due to great contribution to national food security. Crop production is a main source of greenhouse gases (GHGs) and reactive nitrogen (Nr) emissions, quantitatively evaluating the differences in carbon footprint (CF) and nitrogen footprint (NF) of rice–wheat rotation system will benefit the achievement of low-carbon and green agriculture.

Methods Based on farmer's production survey data from middle Yangtze River Basin, the CF and NF of rice–wheat rotation system in middle Yangtze River Basin were estimated using a life-cycle assessment method in the agricultural sector. The proportion of different agricultural inputs and the influence factors in the CF and NF of rice–wheat rotation system were explored.

Results The CF and NF per unit area for rice–wheat rotation systems in middle Yangtze River were CO₂-eq 7728.8 kg/hm² and N-eq 190.6 kg/hm², respectively. The largest fraction of CF and NF of rice–wheat production system was the share of CH₄ emission (39.0%) and NH₃ volatilization (91.8%), respectively. Progressive regression analysis showed that CF and NF of rice–wheat production were mainly affected by diesel and fertilizer. In this study, the scaled planting was negatively correlated with the CF and NF, and a decrease in the CF and NF of rice–wheat production was found in larger farms by 22.6% and 43.9%, respectively, compared to smaller-scale farms. The carbon footprint and nitrogen footprint of rice and wheat production system increased significantly with the increase of yield.

Conclusions Developing water and fertilizer saving technology, as well as increasing farm machinery operation efficiencies and developing large-scale farms is an important way for energy saving, emission reduction and green manner agriculture in the middle Yangtze River Basin.