Abstract: Against the background of global climate warming, it is important to explore efficient straw-returning practices that can improve soil quality and crop productivity while enhancing carbon sequestration and reducing greenhouse gas emissions. Such practices are particularly relevant to tobacco-rice rotation systems, which are widely distributed in southern China. A field rotation experiment was conducted with three treatments: no straw returning (CK), conventional chopped straw returning (CS), and accelerated decomposition straw returning (ADS). The comprehensive effects of these treatments on soil multifunctionality (SMF), crop yield, greenhouse gas emissions, and the net ecosystem carbon budget (NECB) were systematically evaluated. Soil and crop responses were examined during both the tobacco and rice seasons, and the annual ecosystem carbon budget was calculated to compare the overall carbon-sink effects of the three treatments. Random forest analysis was also conducted to identify the soil environmental factors associated with annual NECB. The results showed that both straw-returning treatments improved soil multifunctionality. Compared with CK, CS and ADS significantly increased SMF scores during both the tobacco and rice seasons. This result indicated that both conventional chopped straw returning and accelerated decomposition straw returning had positive effects on the overall functioning of the soil. However, the two straw-returning practices differed in their effects on crop yield. The CS treatment did not significantly increase crop yield. In contrast, ADS significantly increased both tobacco leaf yield and rice grain yield. Compared with CK, tobacco leaf yield and rice grain yield under ADS increased significantly by 5.14% and 11.54%, respectively. Therefore, ADS exhibited a greater yield-enhancing effect than conventional chopped straw returning. Straw returning also altered greenhouse gas emissions. Compared with CK, both CS and ADS significantly increased cumulative CO₂ emissions during the tobacco season, with increases of 66.39% and 58.37%, respectively. The increase under ADS was lower than that under CS, but cumulative CO₂ emissions under both treatments remained significantly higher than those under CK. In addition, ADS significantly increased cumulative N₂O emissions during the tobacco season by 34.88% relative to CK. This increase resulted in a significant 31.34% increase in greenhouse gas intensity (GHGI). These results demonstrate that accelerated decomposition straw returning presents a potential environmental risk because it may increase greenhouse gas emissions. Annual carbon-budget accounting showed that ADS significantly increased crop net primary productivity (NPP). The additional carbon fixed through photosynthesis under ADS was substantially greater than the carbon loss associated with greenhouse gas emissions. Consequently, ADS produced the highest NECB among the three treatments. The NECB under ADS reached 588.07 kg ha⁻¹ (expressed as C), representing a significant increase of 280.04% relative to CK. The ADS treatment therefore exhibited the strongest overall ecosystem carbon-sink effect. Random forest analysis indicated that soil pH, mineral-associated organic carbon (MOC), and total nitrogen (TN) were the key soil factors associated with annual NECB (P < 0.05). In conclusion, accelerated decomposition straw returning improved soil multifunctionality and significantly increased tobacco leaf and rice grain yields. It also enhanced annual NECB and strengthened the overall carbon-sink function of the tobacco-rice rotation system. Nevertheless, this practice increased greenhouse gas emissions and therefore presented a potential environmental risk. Considering its combined effects on crop yield and annual net ecosystem carbon balance, accelerated decomposition straw returning still has good potential for application in tobacco-rice rotation regions of southern China. Future studies should combine this practice with greenhouse gas mitigation measures to further coordinate carbon sequestration, crop yield enhancement, and emission control. These findings provide a theoretical basis for promoting scientifically informed straw-returning practices and supporting the implementation of carbon-peaking and carbon-neutrality goals in the tobacco- and rice-producing regions of southern China.