In this study, we utilized an emergy analysis method to examine emergy flow, establish a variety of emergy indices of the social-economic natural subsystem, and evaluate sustainable development and health levels in the ecological-economic system in the Taihu Lake city cluster in 2015. The results showed the following:(1) renewable resources are insufficiently utilized, and the maximum proportion of renewable resources in the total emergy utilization was only 7.95%; (2) non-renewable resources are consumed too extensively, and the minimum proportion of non-renewable resources in total emergy utilization was 56.95%; (3) the traditional agricultural structure in the Taihu Lake city cluster, except the city of Suzhou, must be adjusted urgently because that the minimum proportion of meat and aquatic products in renewable resource products has reached 63.08%; (4) we should accelerate the transformation and upgrading of traditional industries as a minimum of 88.02% are currently producing products from non-renewable resources, primarily cement and steel; (5) we must accelerate the opening up of trade to the outside world, because the maximum proportion of input emergy is only 36.27% and merchandise import and export exhibits a favorable trade balance; (6) the level of waste emission and utilization needs to be improved, because the current maximum ratio of waste emergy to renewable emergy is only 12.8%, and the minimum ratio of waste emergy to total emergy utilization is only 0.19%; (7) within the Taihu Lake city cluster, the city of Huzhou has greater potential for sustainable development, because its sustainable index (ESI) and emergy sustainable development index (EISD) are 1.59 and 2.99, respectively; (8) the city of Suzhou exhibits a low level of health of the cities in the Taihu Lake city cluster, with a health emergy index (EUEHI) and an improved health emergy index (EUEHI') of 8.22 and 1.65, respectively. Based on the above results, this paper proposes some countermeasures to advance the sustainable development of the ecological-economic system in the Taihu Lake city cluster.