Urban systems cannot be fully understood in isolation from the ecological system in which they exist. Past research projects which analysed energy in urban systems have focused on efficiency and conservation and the analysis of energetic flows that interconnect urban economic and ecological systems have not received much attention. The underlying theme of this paper is the application of ecological energetic analysis to bridge that gap. The energy evaluation of Taiwan, and the development of a global classification of ecological economic systems indicate that in less than half a century, Taiwan has changed from a rural country with an economy based on raw commodity production, to one that is highly industrialized with a lower self-sufficiency of emergy use. using a taxonomic approach, Taiwan can further be classified into four urban ecological economic systems: (1) agricultural settlement; (2) surburban industry; (3) urban metropolis; and (4) resource production. The distribution of these four systems also reveals the spatial energetic hierarchy within Taiwan. Finally, in concluding this paper, future directions for continuing research on urban energetic flows are suggested.