Index system for the agricultural eco-environmental quality in Fujian was established by 13 indexes closely related to the quality. The spatial variation figures of agricultural eco-environmental factors in every decades based on GIS were made. The factors values on the province ,districts and counties were analysed. The results showed that the majority factors in Fujian was changed into bad with decade and form northwest to southeast of Fujian. Ratio of cultivated area to total acreage, ratio of grassland area to total acreage, ratio of disaster area, farmland areas per person , pesticide input and fertilizer input was changed into bad with decade . Key words: agricultural eco-environment; assessment factors; temporal and spatial distribution ; Fujian Province