Input-output relation and change of emergy indices of agricultural ecological system in Gansu Province were analyzed with data from 1991 to 2010 by using emergy theory. The results show that: (1) the total emergy of input and output of agricultural ecological system is increasing with a speed of 85% (output) and 21% (input), the total emergy of input is greater than output, indicating that the agriculture in Gansu Province is still in a traditional agriculture stage; (2) in the study period, environment emergy input and economic emergy input account for the total input of agricultural ecological system 27.97%-28.07% and 71.93%-72.03%, respectively, indicating that environmental resources contributes much to the agricultural in Gansu Province, but the development of agriculture is depending on the economic emergy input increasingly; (3) planting emergy output, stock raising emergy output, forestry emergy output, fishery emergy output account for the emergy of gross output from 81.91%,17.46%,0.49%,0.14% in 1991 to 79.12%,19.96%,0.71%,0.21% in 2010, showing that the structure of agriculture in Gansu Province is becoming optimized; (4) the net emergy yield ratio is improving from 0.61 in 1991 to 0.92 in 2010, suggesting that the operation efficiency of ecological system of agriculture in Gansu Province is gradually becoming good, but it is still less than one, the agricultural production is primary an extensive form, relying on inputting a lot of resources to increase production; the emergy investment ratio is around 2.3, the agricultural depends on the environment more strongly; the environment load ratio is maintain from 2.05 to 3.07, it indicates that the environmental pressure of agriculture production is not high, agriculture environment resources can be developed and utilized further; from 1991 to 2010, the emergy sustainable indices rises from 0.22 to 0.34, it belongs to consumptive ecological system of agriculture; the system of production advantage is maintaining from 0.6 to 0.76, it explains that the development level of planting, stock raising, forestry and fishery is balancing; the system stability index of agriculture ecosystem is increasing from 0.50 in 1991 to 0.55 in 2010, reflecting through the adjustment of agricultural structure, Gansu Province agro-ecological system stability gradually strengthened in the years 1991-2010.