Abstract: Rice production is one of the main sources of greenhouse gas (GHG) emissions in China. Aiming at the strategic goals of “carbon peak” and “carbon neutrality,” it is of great significance to explore the key affecting factors and construct a technical system of carbon sequestration and emission reduction in rice production. Aimed at the main rice-producing areas in the middle and lower reaches of the Yangtze River, we conducted positioning experiments, including low-carbon management measures such as no-tillage, deep placement of nitrogen fertilizer, intermittent water-saving irrigation, and combined management of straw and nitrogen fertilizer, to analyze the key influencing factors of carbon sequestration and emission reduction in rice production. Based on a long-term monitoring of GHG emissions from rice fields, we used ¹³C nuclear magnetic resonance technology to analyze the molecular structure of organic carbon functional groups and clarified the mechanism of rice management measures for reducing carbon emissions and increasing carbon sinks. We further evaluated the indirect carbon emissions from rice production under different rice management technologies using the carbon footprint, and clarify the conversion ratio of exogenous straw carbon in rice systems using ¹³C-labeled straw carbon tracing technique. The results of this study showed that regulating the ratio of straw and nitrogen fertilizer could promote the conversion of straw carbon into small molecular functional groups, promote the adsorption of exogenous particulate organic carbon from soil aggregates, and increase the content of intra-aggregate particulate organic carbon by 32.3% in the soil carbon pool compared with those of conventional straw management methods. Intermittent water-saving irrigation technology could reduce methane emissions by 19.9%–21.1% in paddy fields by increasing the abundance of methane-oxidizing bacteria. Low-energy rice field management technologies, such as no-tillage, could reduce fuel and manpower inputs and comprehensively reduce indirect carbon emissions from rice production by 10.5%–16.7%. Compared with the conventional rice straw return mode, management techniques such as intermittent water-saving irrigation and combined straw and nitrogen fertilizer application could increase the exogenous carbon cycle sequestration rate of straw by 57.3%–59.9%. The development of soil aggregate structure, carbon emission functional microorganisms, soil nitrogen substrate concentration, rice production carbon footprint, and crop carbon sequestration are key factors that affect the carbon neutrality of rice production. Establishing a technical system of carbon sequestration and emission reduction from the perspectives of “sinks increase” “emission reduction” “consumption reduction” and “recycling” could promote rice production carbon neutrality by 28.9%–67.6%.