No-tillage with straw mulch is an effective way to achieve soil sustainability. However, the specific redistributions of soil organic carbon composition, stocks, and crop yield remain unclear. The hypothesis that no-tillage had a minor effect on soil organic carbon stocks in 0–50 cm but decreased crop yield compared to plow-tillage under straw return was tested in this study. Soils properties from two decades of rice-wheat rotation field experiment were related to the yield of rice and wheat depending on tillage: 1) plow-tillage without straw return, 2) no-tillage with straw mulch, and 3) plow-tillage with straw return. No-tillage with straw mulch had the highest mean weight diameter of soil aggregates, the contents of macro-aggregates (>0.25 mm) organic carbon, particulate organic carbon (>53 µm), and soil organic carbon across tillage practices in 0–5 cm. However, it decreased the contents of macro-aggregates (>0.25 mm) organic carbon in 5–15 cm, the particulate organic carbon in 5–50 cm, and soil organic carbon in 5–30 cm compared to plow tillage with straw return due to less carbon input from roots and straw. Organic carbon stocks in micro-aggregates (<0.25 mm) and mineral-associated organic matter (<53 µm) did not vary between tillage practices. Hence the soil organic carbon stocks of plow tillage without straw return (48 Mg ha−1) were similar to that of no-tillage with straw mulch (51 Mg ha−1) but lower than that of plow tillage with straw return (57 Mg ha−1) in 0–50 cm. The mean annual yields of wheat and rice under no-tillage with straw mulch (14 t ha−1) were lower than that of plow tillage without straw return (15 t ha−1) and plow tillage with straw return (16 t ha−1). No-tillage-induced high soil bulk densities limited the rice yields. The yield losses of no-tillage with straw mulch were higher in rice than in wheat. The rice yield losses of no-tillage with straw mulch compared to plow tillage with straw return increased with experiment duration due to decreased available nitrogen in 7–14 cm and phosphorus contents in 0–14 cm over time. Conclusively, plow-tillage is more efficient for carbon sequestration and yield increase than no-tillage under straw return in rice-wheat farming by increasing carbon input in deep soils, soil available nutrients, and decreasing soil compactness.
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