A complete accounting of net greenhouse gas balance (NGHGB) and greenhouse gas intensity (GHGI) affected by Fe(III) fertilizer application was examined in typical annual paddy rice-winter wheat rotation cropping systems in southeast China. Annual fluxes of soil carbon dioxide (CO 2 ), methane (CH 4 ) and nitrous oxide (N 2 O) were measured using static chamber method, and the net ecosystem exchange of CO 2 (NEE) was determined by the difference between soil CO 2 emissions (R H ) and net primary production (NPP). Fe(III) fertilizer application significantly decreased R H without adverse effects on NPP of rice and winter wheat. Fe(III) fertilizer application decreased seasonal CH 4 by 27–44%, but increased annual N 2 O by 65–100%. Overall, Fe(III) fertilizer application decreased the annual NGHGB and GHGI by 35–47% and 30–36%, respectively. High grain yield and low greenhouse gas intensity can be reconciled by Fe(III) fertilizer applied at the local recommendation rate in rice-based cropping systems.