To understand the agricultural production dynamics and sustainability in the hilly areas of southeast China, this paper took Dehua county, a typical mountainous area in Fujian province, as an example to quantitatively analyze the changes of input, output, environmental load and sustainability of farmland-livestock systems from 2007 to 2016, and constructed the indicators of waste emergy ratio and environmental pollution emergy negative output. The results showed that the input of the farmland-livestock system in the study area was mainly based on the purchasing emergy, accounting for 68%-79% of the total emergy input, and the emergy of water resources accounted for 21%-31%. The emergy output of livestock systems accounted for more than 72% of the total output. And the emergy density fluctuated between 2.68×1012 and 3.33×1012 sej·m-2, and emergy per person increased from 1.23×1016 sej to 1.72×1016 sej. The net emergy yield ratio decreased by 40%, and the environmental load increased significantly, which could have been maintained since 2015. The emergy sustainability index fell rapidly from 1.14 to 0.42 after a brief rise in 2007-2010. From the indicators of construction, the proportion of system waste emergy decreased, and environmental pollution emergy output decreased by about 22%. In terms of comprehensive economic benefits and waste utilization, the sustainable development of Dehua county has gradually improved in recent years. Dehua county is currently adjusting its output structure of farmland-livestock system. It should increase the amount of feedback emergy in the system, control fertilizer and feed input, and improve waste utilization to achieve sustainable development.