The role of agriculture in greenhouse gas emissions and carbon neutrality is a complex and important area of study. It involves both carbon sequestration, like photosynthesis, and carbon emission, such as land cultivation and livestock breeding. In Shandong Province, a major agricultural region in China, understanding these dynamics is not only crucial for local and national carbon neutrality goals, but also for global efforts. In this study, we utilized panel data spanning over two decades from 2000 to 2022 and closely examined agricultural carbon dynamics in 16 cities of the Shandong Province. The method from the Intergovernmental Panel on Climate Change (IPCC) was used for calculating agricultural carbon sinks, carbon emissions, and carbon surplus. The results showed that (1) carbon sink from crops in the Shandong Province experienced growth during the study period, closely associated with the rise in crop yields; (2) a significant portion of agricultural carbon emissions was attributable to gastrointestinal fermentation in cattle, and a reduction in the number of stocked cattle led to a fall in overall carbon emissions; (3) carbon surplus underwent a significant transition in 2008, turning from negative to positive, and the lowest value of carbon surplus was noticed in 2003, with agriculture sector reaching the carbon peak; (4) the spatial pattern of carbon surplus intensity distinctly changed before and after 2005, and from 2000 to 2005, demonstrating spatial aggregation. This research elucidates that agriculture in Shandong Province achieved carbon neutrality as early as 2008. This is a pivotal progression, as it indicates a balance between carbon emissions and absorption, highlighting the sector’s ability in maintaining a healthy carbon equilibrium.