Effective livestock manure management is crucial for carbon neutrality. Scientific accounting methods and integrated management strategies can help guide reductions in carbon emissions and promote green development. To reduce greenhouse gas emissions by livestock manure, this study analyzed current accounting systems and focused on the complete chain of “collection-treatment-storage-use-returning” of manure based on the theoretical framework of greenhouse gas emissions accounting in the IPCC 2019 Guidelines. Combined with a life cycle assessment, the accounting list and boundaries were clarified, and the whole chain of livestock and poultry manure greenhouse gas accounting methodology system was proposed. Using swine breeding as a case study, this study evaluated the carbon emission reduction and sequestration effect of the whole manure chain using a typical technology model and a typical technological framework. It predicted the carbon reduction potential and sequestration benefits of utilizing swine manure in 2025 and 2030 in four scenarios. The findings indicated that the greenhouse gas emission factor of the whole chain of the six typical swine manure utilization modes in China was −48.82–40.54 kgCO2et−1. In 2022, the net greenhouse gas emissions from swine manure in China totaled approximately 2.0 × 107 tCO2e, with manure resource utilization reducing emissions by 3.2 × 107 tCO2e. Our projections suggest that emissions from swine manure in China may range from −1.8 × 107 to 1.3 × 107 tCO2e by 2025 and from −3.1 × 107 to 4.5 × 106 tCO2e by 2030. This can help guide optimal greenhouse gas emission reduction pathways for livestock and poultry farming and aid in the formulation of policies.