Based on the China net primary productivity data of vegetation from 2006 to 2019, the distribution data of three staple crops, and agricultural production inputs, this article estimates the carbon sink, agricultural carbon emissions, and carbon footprint of China’s three staple crops, and analyze the spatial and temporal patterns of carbon sinks in the three staple crops. The results show that 1) from 2006 to 2019, the total carbon sequestration of the three staple crops in China continues to increase, with rice, maize, and wheat accounting for 41.92%, 38.62%, and 19.46%, respectively. The carbon sequestration capacity of three staple crops far exceeds the carbon emissions caused by agricultural production factors, with a ratio of 5.37:1, indicating that the China agricultural ecosystem has a strong carbon sequestration capacity. 2) The total agricultural carbon emissions in China have continued to increase, but the growth rate has decreased. Fertilizer and diesel are the main carbon sources. 3) The ecosystem of three staple crop farmlands shows a significant carbon ecological surplus. The carbon footprint in 2019 is 17.55×10⁶ hm², accounting for 18.62%, which means that the CO₂ emissions from the production of the three staple crops farmland system are reduced to less than 1/5 of the China three staple farmland to absorb. The results can help clarify their position in the carbon cycle and provide important scientific basis for promoting agricultural carbon emission reduction, achieving “carbon peak” in 2030 and “carbon neutral” in 2060.