Traditional agricultural systems are under severe threat from modernization, technological and economic changes, while substitution of traditional agriculture with so—called modern agriculture has caused serious non—point source pollution. Ecological footprint, though an approach to measure ecological sustainability, fails to reveal the true environmental condition of the traditional agricultural areas. This paper attempted to establish an enhanced emergy—based ecological footprint (EEF) which could include all the flows of ecosystem services that the local inhabitants had consumed, thus making EEF a better indicator of the regional sustainability. This new approach was then applied to evaluate the sustainability of Congjiang County in Guizhou Province, a typically traditional agricultural area in China. Results showed that the local biocapacity could only meet 64% of the total consumption needed by the local inhabitants, leaving an ecological deficit of 5.2327 gha per capita. This analysis was contrary to earlier findings obtained through the conventional method that Congjiang County was characterized by a small ecological reserve. Disaggregated analysis revealed that the consumption of waste treatment and erosion control services occupied a considerable proportion of the local ecological footprint, indicating that regional sustainability was under serious threat from waste discharge and soil erosion.