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The emergy concept, integrated with a multi-objective linear programming method, was used to model the agricultural structure of Xinjiang Uygur Autonomous Region under the consideration of the need to develop a low-carbon economy. The emergy indices before and after the structural optimization were evaluated. In the reconstructed model, the proportions of agriculture, forestry and artificial grassland should be adjusted from 19:2:1 to 5.2:1:2.5; the Emergy Yield Ratio (1.48) was higher than the average local (0.49) and national levels (0.27); and the Emergy Investment Ratio (11.1) was higher than the current structure (4.93) and that obtained from the 2003 data (0.055) in Xinjiang Uygur Autonomous Region, the Water Emergy Cost (0.055) should be reduced compared to that before the adjustment (0.088). The measurement of all the parameters validated the positive impact of the modeled agricultural structure. The self-sufficiency ratio of the system increased from the original level of 0.106 to 0.432, which indicated a better coupling effect among the subsystems within the whole system. The comparative advantage index between the two systems before and after optimization was approximately 2:1. When the mountain ecosystem service value was considered, excessive animal husbandry led to a 1.41 × 1010 RMB·a−1 indirect economic loss, which was 4.15 times the GDP during the same time period. The functional improvement of the modeled structure supports the plan to “construct a central oasis and protect the surrounding mountains and deserts” to develop a sustainable agricultural system. Conserved natural grassland can make a large contribution to the carbon storage; and therefore, it is wise alternative that promote a low-carbon economic development strategy

Emergy-Based Adjustment of the Agricultural Structure in a Low-Carbon Economy in Manas County of China