Abstract: Farmland transfer, supported by both the national and local governments, has largely promoted the transformation of agricultural management and modernization. Specifically, the increasing scope and scale of farmland transfer dramatically changed the industrial structure and input-output of agriculture. Thus farmland transfer has a significant effect on the agro-ecosystem. To assess eco-environmental effects of the transformation of the mode of agricultural management due to farmland transfer, this study analyzed three aspects of farmland transfer ― production efficiency, environmental impact and overall sustainability of agro-ecosystems. This was done in a case study of Rongchang County in Chongqing, China. To do that, the input-output of ordinary farmers and agricultural contractors, which respectively represented the agricultural management patterns before and after farmland transfer, was analyzed. The emergy evaluation method used proved to be effective in analyzing the efficiency and sustainability of ecosystems. Emergy evaluation method overcame the weakness of traditional methods of energy analysis as it integrated different forms of energy into a common physical basis known as solar emergy. This method took multiple important factors into consideration (e.g., natural resources, labor and ecosystem services), generally neglected in other similar methods. The results showed that the input for purchasing resources decreased by 70.48% while emergy output increased by 2.15% after farmland transfer. Thus emergy yield ratio (EYR) changed from 0.01 before farmland transfer to 0.04 after that, which represented an increase of 300.00%. This increase was mainly due to agricultural machinery input rather than labor force input, which lowered the overall input and increased the efficiency of production. For a single input item, when its’ renewability factor was less than that of the ecosystem, decreasing input reduced the environmental loading ratio (ELR); for the item, whose renewability factor was higher than that of the ecosystem and vice versa. The decline in labor force together with the increase in pesticide and fertilizer use increased the environmental load of an ecosystem. Thus ELR changed from 0.12 to 0.65, which was a rise of 441.67% after farmland transfer. Emergy sustainability index (ESI) changed from 0.08 to 0.06, a decline of 25.00%. This indicated that the moderate increase in farmland for a household significantly reduced the cost of agricultural production and increased the market competitiveness of agricultural products. However, in modern agriculture, the drive for increased output and added values of agricultural products had substantially increased the use of pesticides and fertilizers. This has in turn intensified the potential risks of agro-ecosystems. In summary, an intensive agricultural development mode should be carefully selected and adopted in order to achieve the goals of sustainable agro-ecosystems. Therefore national policies should pay more attention to the selection of agricultural modes during the process of farmland transfer and scaling farmland cultivation.