The health evaluation of urban ecosystem has been hotspots in current research. In this paper, the indicators for the assessment of urban ecosystem health were sifted through the almanac as well as bulletin data via principal component analysis method and then an evaluation model of urban ecosystem health was constructed via fuzzy mathematics to evaluate urban ecosystem health of Nanjing during the period from 2001 to 2011. The results indicated that the urban ecosystem health of Nanjing was gradually developing from the level of health to especially health from 2001 to 2011; and during this period, the vigor, organization, resilience factor of Nanjing ecosystem might manifest strong capability to maintain current situation or promote it into the advanced health level while the capability of urban ecosystem service and human health factor in serious situation and with large fluctuation might seriously constrain the enhancement of health level of Nanjing ecosystem.