Abstract: Farmland ecosystem is an important carbon source and carbon pool.Estimating the carbon emission and absorption of a farmland ecosystem is significantly important in making strategies to reduce greenhouse gas emission.Based on the statistical data of crop yield, cropland areas and agricultural inputs in the period from 1991to2010, the amounts of carbon absorption and emission of farmland ecosystems in Fujian were calculated, and the spatial-temporal variations and impact factors of carbon absorption and emission were also analyzed.The results indicated that, the total amount of carbon absorption has a decreasing tendency, which reduced from 1 161.14×104t in 1991 to 672.13×104 t in 2010.The total amount of carbon emission has an increasing tendency, which increased from 114.05×104t in 1991 to 195.10×104t in 2010.The amount of carbon sequestration has a decreasing tendency, which reduced from 1 047.09×104 t in 1991 to 477.03×104 t in 2010.The carbon absorption per unit area of arable land also showed a descending trend, however the carbon emission per unit area of arable land remained almost no changes.In 2010, the amounts of carbon absorption and carbon sequestration were both maximum in Nanping, and the amount of carbon emission was maximum in Zhangzhou.However, the minimum in the amounts of carbon absorption, carbon emission and carbon sequestration were all in Xiamen.The results in correlation analysis showed that, carbon absorption was significantly positive correlated with the yields of rice, wheat and sugarcane.Carbon emission was significantly positive correlated with the potassic fertilizer, compound fertilizer, pesticide, power and fuels consumption.The results will serve as a strong support for the development of low carbon agriculture of Fujian Province.