Abstract: A research was conducted on the comprehensive assessment of agricultural eco-economic systems in Fujian Province. Using GIS & RS along with mathematical methods, a series of data collection and discrimination of original indicator data was performed. A frame of comprehensive indicator system of assessment of agricultural eco-economic system (with 5 levels including top, status, norm, variable and element) was set up. Original combination indicators were transformed into comparable indices by the de-dimensionalization. The indicator weight was ascertained based on entropy weight method and the indicator system gradually converged. Using GIS platform, the spatial distribution of the agricultural eco-economic levels for the cities/counties were analyzed and extreme phenomena exposed. Such information can be used as a guiding reference at different levels of agricultural decision-making.