Abstract: Exploring the mechanisms underlying high-yield formation and its carbon budget balance in rice ratooning is of significant importance for further unlocking the yield potential. This study was conducted in Putian, Fujian province (119°07′E, 25°18′N). Two varieties with varying growth durations were utilized to examine the yield formation of the main crop (MC), ratoon season rice (RSR), and the counterpart single cropping rice (LR). The dynamics of rhizosphere microorganisms, and the net ecosystem carbon balance (NECB) in paddy fields, as well as the underlying associated mechanisms influencing these processes were also investigated in 2023 and 2024. The results demonstrate that the average daily yield of RSR was 46.37% to 82.66% and 42.35% to 86.61% higher compared to that of MC and LR synchronously heading with RSR, respectively. This discrepancy was attributed to the higher dry matter transport efficiency of RSR by 41.49% and 41.44%, and the greater amount of dry matter transferred to the panicles compared with MC and LR, respectively. Compared to that of MC and LR, the allocation of photosynthetic products to the below-ground parts (roots and soil) in RSR decreased by 56.05%−58.79% and 52.14%−53.19%, respectively, with the allocation proportion reduced by 49.39%−54.11%, and 49.28−49.40%, respectively. Conversely, compared to MC and LR, the allocation of photosynthetic products to the panicle organs of RSR increased by 5.10%−17.67% and 19.48%−20.30%, respectively, with the allocation proportion reduced by 21.04%−31.04% and 27.49%−29.14%, respectively. This in turn resulted in a higher harvest index and average daily yield of RSR. Moreover, the analyses of greenhouse gas emission intensity (GHGI) and NECB in paddy fields demonstrated that the daily average carbon emission index of MC+RSR system decreased by 52.12%−60.96% compared with that of LR counterpart. The comparative analysis reveals significant differences in carbon sink capacities between cropping patterns. The MC+RSR system demonstrates robust carbon sequestration performance, achieving a carbon balance ranging from 17.78 to 32.85 t(CO₂-eq)·hm^-2. In contrast, the counterpart LR exhibits relatively weaker carbon sink functionality with a surplus of only 5.70 to 11.67 t(CO₂-eq)·hm^-2. This divergence stems from two key mechanisms: effectively extending the utilization period of light and thermal resources through its unique growth cycle configuration (main crop-ratooning rice), and increasing a carbon fixer, but decreasing the carbon decomposers in RSR rhizosphere soil, relative to that in MC and LR, respectively. These findings provide an evidence for advancing agricultural carbon neutrality technologies, and for achieving the goals of agricultural low-carbon, green and sustainable development.