After the discussion of accomplishments of ecological urban construction in Suzhou City, the current ecological urban construction in Suzhou has been compared with the national standard for ecological urban construction. According to the actual situation of Suzhou urban construction, the health evaluation index system and standards for urban eco-system have been established based on natural, economic and social sub-system. By using mean square deviation, indexes’ weights have been identified. After the quantitative research on the health condition of urban eco-system in Suzhou City from 2004 to 2008, it has found key problems existing in its ecological urban construction. The results show that Suzhou urban eco-system develops well in general, but the three sub-systems are coordinated with each other moderately, and natural sub-system suffers severe pressure.