Comprehensive accounting of carbon emissions and carbon sinks in the agricultural sector is crucial for China to achieve its carbon neutrality goal as early as possible. This paper develops a comprehensive and scientific accounting system to recalculate China’s agriculture sector’s carbon emissions and sinks from 1995 to 2020, taking into account both resource inputs and productive activities. Subsequently, the STIRPAT model is employed to predict alterations in carbon emissions and sinks across different scenarios. The results show that energy consumption, chemical inputs, and farmland soil management have surpassed livestock and poultry breeding as the main contributors to agricultural carbon emissions. Furthermore, this paper classifies 31 provinces in China into five distinct types based on the variations in agricultural carbon emissions and carbon sinks. These types include carbon sink-dominated regions, paddy planting-dominated regions, livestock farming-dominated regions, resource inputs-dominated regions, and composite factor-dominated regions. In addition, the extent of agricultural technology and the magnitude of agricultural development are the key factors impacting China’s agricultural carbon emissions and carbon sinks, respectively. Prior to 2045, agricultural carbon emissions must be directly reduced as much as possible, and their source must be controlled; following that year, the role of carbon sequestration will become more prominent, and the active development of agricultural carbon sinks will be more beneficial in achieving agricultural carbon neutrality.