The rapid economic growth accompanied by health concerns and other global environmental problems in cities and regions has boosted the popularity of the ‘urban metabolism’ topic among academics and policymakers. Currently, 56.2% of the world's population lives in cities, accounting for 80% of the global GDP. It is projected that the current trend for world economic growth complemented by population growth and migration will continue affecting the resource production and consumption in cities and the impact this has on other urban areas. Here, we developed a new model approach that combines emergy input-output tables with ecological network analysis to investigate urban metabolism generally, and applied it to Vienna, Austria. This novel approach allows researchers to study the hierarchy of sectors and functional relationships along all possible metabolic paths of ecological and socio-economic flows exchanging in an urban economy and between the urban economy and its environment. Then, using system-level analyses (flow and contribution analyses) we determined the status of the system components. Finally, the critical components responsible for the status (distribution structure of each industry) and emergy consumption of the other sectors were identified using pairwise control and utility analyses. The results showed that the “agriculture, forestry and fishing” and “mining and quarrying” sectors had the lowest ability to receive financial inputs from the other sectors, reflecting a shortage of agricultural and mining products to meet consumers' demand. Moreover, “agriculture, forestry and fishing” had the highest energy dependence on the other sectors, indicating the lack of self-sufficiency in energy use and the inability of this sector to deliver energy effectively to consuming sectors. This also implies the importance of this sector in achieving the energy efficiency improvement and economic development goals for consumer cities. This work contributes to the existing literature on ecological network analysis via an introduction of the two-step approach that combines the diagnosis of low activity components in the system taken from traditional ecological network analysis with the novel identification of components behind the low activity of the other components. In addition, direct and indirect control, and indirect utility analysis were introduced for the analysis of the impact of the direct energy and indirect pairwise economic control and relational interactions of sectors in cities. Finally, this work explored the inner workings of the service part of the urban economy to reveal the role each tertiary sector plays in the development of primary and secondary sectors of an urban economy. The model developed in this study will provide support for city managers and policymakers to guide resource consumption towards an efficient and sustainable urban metabolic system worldwide.