Straw return can enhance crop yields and nitrogen fertilizer use efficiency (NFUE) in paddy-upland rotation systems. However, straw return in wetland rice systems can significantly increase CH4 emissions, which could be alleviated if the straw is converted to biochar before incorporation. This study investigated the effect of different crop residue management strategies on NFUE and greenhouse gas (GHG) emissions in a paddy-upland rotation over a four-year field experiment. We compared two treatments where all crop residues were removed (no N fertilizer (PK), recommended N fertilizer (NPK)) with three different methods of straw return. This included (i) direct straw return (NPK+S/S), where all crop residues were directly applied to the field after harvest; (ii) straw return as biochar (NPK+B/B), where all crop residues were converted into biochar before incorporation; (iii) straw return as biochar in the rice season and direct straw return in the oilseed rape season (NPK+B/S). Four-year crop yields, NFUE, two-year ammonia (NH3) volatilization, and GHG emissions were determined. The results showed that compared with the NPK treatment, straw and biochar return increased rice and oilseed rape yields by 0.41–0.80 t ha−1 and 0.24–0.33 t ha−1, respectively, and the annual NFUE by 4.3–6.9%. Direct straw return (NPK+S/S) did not significantly affect annual NH3 volatilization, but significantly increased cumulative N2O emissions (by 27.3%), CH4 (by 132.4%), global warming potential (GWP, by 75.2%) and greenhouse gas emissions intensity (GHGI, by 61.1%), respectively. In contrast, converting crop residues into biochar before incorporation significantly reduced annual NH3 volatilization and N2O and CH4 emissions. Compared with the NPK+S/S treatment, the NPK+B/B and NPK+B/S treatments reduced cumulative N2O by 20.5–26.7% and CH4 emissions by 56.5–65.9% with the corresponding reduction in GWP value (42.3–50.4%) and GHGI value (44.3–52.6%). Considering biochar production cost, we recommended straw return as biochar in the rice season and straw mulching in the upland season as a measure to increase crop yields and NFUE while reducing GHG emissions in the paddy-upland rotation.
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