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Deep straw incorporation, as a sustainable agricultural practice, reduces carbon dioxide (CO 2 ) emissions and mitigates global warming. CO 2 dynamics across soil layers are influenced by the vertical distribution of soil moisture, especially in the context of frequent extreme rainfall events. However, CO 2 dynamic responses to varying soil moisture under deep straw incorporation remain poorly understood. Here, two rainfall patterns (30 events of 10 mm each and 4 events of 75 mm each) and three straw incorporation treatments (CK: without straw incorporation, shallow: straw incorporation into 0–20 cm layer, and deep: straw incorporation into 0–40 cm layer) were established in a soil column simulation experiment. CO 2 concentrations, CO 2 fluxes, soil moisture, readily oxidizable organic carbon (ROC), and microbial extracellular enzyme activities were measured during the experimental period. The cumulative CO 2 emissions of deep straw incorporation decreased by 26.4%–36.3%, while the average CO 2 concentration in 20–40 cm of deep straw incorporation was 36.3%–82.3% higher than that of shallow straw incorporation. The increment of cumulative CO 2 emissions derived from 75 mm rainfall events under deep straw incorporation (15.5%–16.6%) was less than that under shallow straw incorporation (20.6%–23.8%). Meanwhile, the ratio of CO 2 ‐C to straw‐C inputs decreased from 16.9% to 36.4% under shallow straw incorporation to 8.6%–17.6% under deep straw incorporation when stimulated by 75 mm rainfall events. Deep straw incorporation enhanced CO 2 concentrations of 20–40 cm through increased extracellular enzyme activities and ROC content, yet the 0–20 cm layer acted as a barrier that impeded upward CO 2 transport. The synergistic effect of straw incorporation and 75 mm rainfall induced a CO 2 concentration pulse in 0–20 cm and more intense emissions to the atmosphere under shallow incorporation. Our findings elucidate that deep straw incorporation is beneficial to C sink in rainfed agroecosystems, providing new insights for straw management practices under climate change.