Ecosystem health has been a hot topic of the urban ecology in the recent years. In combination with the ecosystem service function of the urban ecosystem, a theoretical framework and methodology of the urban ecosystem health assessment based on emergy were proposed and the characteristics and comparative implication of the temporal variation of the health level of the city were also outlined. Four factors, including vigor (V), organizational structure (O), resilience (R), and function maintenance (F), were collected to construct a novel emergy-based index on urban ecosystem health (Emergy-based Urban Ecosystem Health Index: EUEHI). Based on the EUEHI of Baotou and in comparison with the EUEHI of other five cities, Baotou city′s health level continuously increased from 2000 to 2004, despite of a relatively low level on the whole due to an emphasis on the resource structure adjustment and utilization efficiency, which makes a better service function for the integrated urban ecosystem. Meanwhile, as a traditional industrial city, Baotou city was characterized by the disorganizational structure and large environment pressure, as well as low ecosystem recovery capability. Therefore, lowering gradually the environmental threat is necessary to eliminate the disturbance of the urban ecosystem, thus enlarging the urban ecosystem carrying capacity and promoting the power of urban ecosystem service function.