Regarding various energy and materials flowing in the urban ecosystem and the merit of emergy as an embodied energetic equivalent for integrated ecological economic evaluation, an evaluation framework of emergy-based urban ecosystem health indicators (UEHIem) was established in view of five aspects including vigor, structure, resilience, ecosystem service function maintenance and environmental impact to depict the urban ecosystem health states. Further, set pair analysis (SPA) was employed to assess the urban ecosystem health level based on the UEHIem, by which the approximate degree of real index set to the optimal one was defined and evaluated to describe the relative health state of the concerned urban ecosystems. Choosing twenty typical Chinese cities in 2005 as cases, we evaluated and compared their urban ecosystem health levels based on UEHIem and SPA. The results showed that health levels of Xiamen, Qingdao, Shenzhen and Shanghai are pretty well, while those of Wuhan, Harbin, Yinchuan, Beijing and Urumchi are relatively weak. Moreover, the relative health levels were analyzed by SPA to discern the influences of the mentioned five aspects on the UEHIem. It is concluded that emergy synthesis combined with SPA can serve as an effective relative-measure to compare different ecosystem health levels of urban ecosystems.