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 conducted based on the National Agricultural Experimental Station for Soil Quality in Xuzhou, Jiangsu Province from 2021. In 2023, five treatments of the experiment were selected: chemical fertilization (CK), and combined applicaitons of chemical fertilizers with wheat straw (ST), with biochar (BC), with organic fertilizer (OF), and with green manure (GF). This study investigated 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 of sweet potatoes ranged from 1 818.02 kg·hm⁻² to 3 811.72 kg·hm⁻², and carbon sequestration by storage roots ranged from 2 718.69 kg·hm⁻² to 4 299.93 kg·hm⁻² for each treatment. NPP of sweet potato 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) soil. 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 OF treatment significantly decreased the cumulative amount of CO₂-C emitted from soil heterotrophic respiration, and significantly increased the cumulative amount of CO₂-C emitted from autotrophic respiration. Regression analyses showed that soil respiration rate increased with increasing water vapor flux and temperature. Spearman analyses showed that the cumulative CO₂-C emitted from soil heterotrophic respiration was influenced by aboveground carbon content, soil water content, and subsurface soil 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 treatment had the best effect. However, at the same time, the cumulative CO₂ emission from soil respiration was also the highest under OF treatment. 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.