Abstract: The Energy flows of agro-ecological system were analyzed quantitatively in Changting County of Fujian Province by using the theory and methods of Energy analysis. The 10 Energy indices, including Energy yield ratio (EYR), Energy investment ratio (EIR), environment carrying capacity (ECC), Energy—based sustainability index(ESI), system dominant degree (SDD) and system stability degree (SSD) are analyzed．EIR, EYR, ECC, ESI, SDD, SSD was 1.91, 11.40, 2.21, 19.10, 0.53 and 0.90 respectively in 2005. The result showed that this region is in the stage of transformation from traditional agriculture to modern agriculture. In order to promote the sustainable development of agriculture in the region, suitable measures should be taken, that is, to regulate the input in agriculture, to increase utilization ratio, to stimulate academic research, and to improve the productivity of agricultural economic systems.