Objectives Wheat-soybean system is a popular gramineae-legume multiple cropping system in Huang-Huai-Hai region, China. Comprehensive evaluation of the net carbon emissions of this cropping system is of great significance for carbon sequestration and emission reduction in farmland of China. Thus, in search for sustainable fertilization method that concurrently improves yield and lower carbon emissions, we studied the effects of different fertilizers on crop yield and net carbon emissions in a 30-years wheat-soybean system.

Methods The seven fertilization treatments in the experiment were sole cattle manure (M); balanced chemical NPK fertilizer (NPK); combined application of NPK with cattle manure (NPKM), rapeseed cake (NPKC), or both (NPKMC); chemical NP plus wheat straw (NPS); and no fertilizer application (control, CK). The net carbon emissions under each fertilization treatment was estimated as the total direct greenhouse gas (N₂O and CH₄) emissions in the field, indirect carbon emissions caused by agricultural inputs and soil organic carbon sequestration. The net greenhouse effect in each fertilization treatment was evaluated as the total carbon emissions from crop yield and soil organic matter (SOM).

Results Compared with NPK treatment, the NPKM, NPKC and NPKMC treatments increased soybean yield by 31.0%, 16.8% and 24.0%, respectively, while soybean and wheat yields under M and NPS treatments were not significantly different from those of NPK. Compared with NPK treatment, M, NPKM and NPKMC treatments increased direct greenhouse gas (GHG) emissions in the field by 49.4%, 17.7% and 12.4% respectively and annual soil organic carbon sequestration by 282.2%, 137.3% and 169.1% respectively. The indirect carbon emissions in M and NPKM treatments were similar to that of NPK, whereas those of NPS, NPKC and NPKMC were lower than that of NPK treatment. The carbon emissions caused by fertilizer input accounted for the largest proportion of total indirect emissions, followed by electricity for irrigation and mechanical diesel. All treatments, except M, were carbon source, but the net carbon emissions under combined application of NPK and organic materials were lower than that of NPK only. The carbon emission intensity and ratio of δGHG/δSOM under combined application of NPK and organic materials were lesser than that of NPK by 36.5%‒113.2%, and 69.4%‒93.2%, respectively.

Conclusions Combined application of NPK and organic fertilizer (cattle manure or cake fertilizer) could reduce the net greenhouse gas emission while ensuring optimal crop yield in wheat-soybean cropping system in Huang-Huai-Hai region.