Eco-economical division is a new model for integrated development of social economy, enviroment protection and natural resources utilization within a certain region. According to the eco-economic theory, 53 specific indexes suitable for classification of eco-economic systems of the Miyun reservoir watershed in Beijing were selected. These specific indexes were taken for classifiying the eco-economic systems of 38 townships at Miyun reservoir watershed and 5 methods of non-overlapping intrinsic hierarchical agglomerate analysis were adopted. The results indicate that the Ward's hierarchical classification method is better than the others during this classification. The whole region was divided into 5 eco-economic regions and 8 sub-regions by using this method, and the results was good and objective. In addition, the special causes of eco-economic characteristics and development in every eco-economic region were analyzed. It provides scientific base for optimizing eco-economic system structure at the Miyun reservoir watershed.