Abstract: The carbon stocks of sweet potatoes and soil respiration were investigated following different types of organic amendments to lay a foundation for further research on carbon sequestration and emission effects in sweet potato ecosystems. Fertilization experiments for the sweet potato–wheat rotation system were based on the National Agricultural Experimental Station for Soil Quality in Xuzhou, Jiangsu Province. For 2023, five treatments were selected for this experiment: chemical fertilizers (CK), chemical fertilizers combined with wheat straw (ST), chemical fertilizers combined with biochar (BC), chemical fertilizers combined with organic fertilizer (OF), and chemical fertilizers combined with green manure biomass returned to the field (GF). This study focused on investigating the yield, aboveground biomass, and carbon content of sweet potatoes during the harvest. Furthermore, the net primary productivity (NPP) was estimated to characterize the effects of carbon sequestration by plants. Soil samples were collected during harvest to analyze physicochemical properties and carbon fractions. Soil respiration rates were monitored during the reproductive period. The results were as follows: 1) compared to the CK treatment, the ST, BC, OF, and GF treatments significantly increased soil total organic carbon content; the ST and GF treatments significantly decreased soil dissolved organic carbon (DOC) content by 21.3% and 25.2%, respectively, whereas the OF treatment significantly increased DOC content by 12.8%. 2) Carbon sequestration by vines has ranged from 1 818.02 kg·hm⁻² to 3 811.72 kg·hm⁻², and carbon sequestration by storage roots has ranged from 2 718.69 kg·hm⁻² to 4 299.93 kg·hm⁻² for each treatment. NPP in sweet potato has ranged from 9 559.16 to 14 392.58 kg·hm⁻². The BC and GF treatments decreased NPP by 22.5% and 19.9%, respectively, whereas the OF treatment elevated NPP by 16.7% compared to the CK treatment. Correlation analysis showed that carbon sequestration by storage root was mainly positively correlated with soil DOC content (P<0.05), and it was negatively correlated with the compactness of the subsurface layer (22.5−40.0 cm). 3) The cumulative emissions of CO₂-C ranged from 5 738.84 kg·hm⁻² to 11 257.23 kg·hm⁻² during the growth period of sweet potato among these treatments, wherein the OF treatment had the highest emissions. Compared with the CK treatment, the cumulative amount of CO₂-C emitted from soil heterotrophic respiration significantly decreased, and that emitted from autotrophic respiration significantly increased under the OF treatment. Regression analyses showed that soil respiration rate increased with increasing water vapor flux and temperature. Spearman analyses showed that the cumulative CO₂-C emitted by soil heterotrophic respiration was influenced by aboveground carbon content, soil water content, and subsurface compactness. In contrast, the yield and carbon emission efficiency of storage roots were the main factors influencing the rate of soil autotrophic respiration. In summary, this study clarified the effects of returning different organic materials on the carbon sequestration of sweet potatoes, and the OF application had the best effect. However, at the same time, the cumulative CO₂ emission from soil respiration was also the highest. The drivers of heterotrophic and autotrophic respiration in the soil are different and require further investigation. These results provide a theoretical reference and scientific basis for creating green and low-carbon technologies for typical crops in the region.