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The agricultural economy of Fujian Province has grown rapidly since the 21st century. In order to evaluate the impact of economic growth on the sustainability of agro-ecosystems, emergy analysis was used to study the dynamics of agro-ecosystem and its sustainable development capacity in Fujian Province from 2000 to 2016. The results showed that the total emergy input and output of agro-ecosystem in Fujian Province presented an upward trend from 2000 to 2016. Environmental loading ratio (ELR), emergy investment ratio (EIR) and per capita emergy used (EUPP) all showed a growth trend. The ELR and EIR are significantly positively correlated with GDP per capita. Emergy self-sufficiency ratio (EYR), emergy dollar ratio (EDR), emergy sustainability index (ESI) and emergy index for sustainable development (EISD) showed a downward trend from 2000 to 2016. The results suggested that agro-ecosystem of Fujian Province is a sustainable development system, but the sustainability of system is low and gradually declining. In the future, the sustainable development of agro-ecosystem in Fujian Province can be promoted by replacing traditional fertilizers with organic fertilizers, using clean energy to generate electricity, developing ecological agriculture, increasing investment in science and technology, and controlling population growth. Keywords: Agro-ecosystems, Emergy analysis, Sustainable development indices