Abstract: This paper used emergy analysis method at unit county scale to study the spatial variation in agro-ecosystem in Fujian Province. The paper established 13 emergy indicators grouped into 4 levels of agro-ecological economic systems, and selected major emergy evaluation indices by component analysis. Indices and ranks were created for agro-ecosystem development at different aspects for the 67 counties using GIS platform. The result shows clear spatial variations in the agro-ecosystems. These variations are driven by geographical and hypsographical factors. Low-lying coastal counties / cities have absolute advantage in agro-economic development and farmers’ living standards. These advantages are, however weak and can therefore be hardly sustainable. Some inland mountainous counties / cites have obvious regional comparative advantage in natural agro-environmental condition and sustainable development capacity. Based on the results, these are spatially classified into 4 groups. The study provides scientific bases for regional agro-ecological planning and management decisions at all ranks.