Using the agricultural production statistical data of Chongqing in 2006–2015, we estimated and analyzed the carbon emissions, carbon absorption and carbon footprint of the farmland ecosystem aiming to explore the factors contributing to carbon emissions and carbon absorption changes. The results showed that, among all the emission factors, the amount and proportion of nitrogen fertilizer were the highest, about 50%, with a declining trendency year by year, from 51.35% in 2006 to 47.32% in 2015. The carbon absorption of the whole growth period of rice, the most popular corp in Chongqing, was 4.099 5×106 t, accounting for 39.16% of all the carbon absorption. The proportion of farmland ecosystem carbon footprint showed a downward trend, from 19.78% in 2006 to 17.44% in 2015, which demanded approximately 1/5 of the cultivated land sown to balance. This indicates that the Chongqing farmland ecosystem had been in a carbon surplus state, with 2.727 2×106 hm2 in 2015. And, it also shows that the carbon sink function of farmland ecosystems in Chongqing had been enhanced.