Prevailing hypotheses recognize cities as super-organisms which both provides organizing principles for cities and fills the scalar gap in the hierarchical living system between ecosystems and the entire planet. However, most analogies between the traits of organisms and cities are inappropriate making the super-organism model impractical as a means to acquire new knowledge. Using a cluster analysis of 15 traits of cities and other living systems, we found that modern cities are more similar to eukaryotic cells than to multicellular organisms. Enclosed industrial systems, such as factories and greenhouses, dominate modern cities and are analogous to organelles as hotspots that provide high-flux goods and services. Therefore, we propose a super-cell city model as more appropriate than the super-organism model. In addition to the theoretical significance, our model also recognizes enclosed industrial systems as functional components that improve the vitality and sustainability of cities.