Abstract: A healthy innovation ecosystem should be productive, sustainable, and diverse. From the perspective of enterprises, it screens the indexes through the Delphi method, develops quantifiable third level evaluation indexes and determines the weights of each level to construct an innovation ecosystem health evaluation index system including three first level indexes such as productivity, adaptability and diversity and nine second level indexes such as production efficiency, innovation output, resistibility and species diversity. Taking the manufacturing industry clusters in Hunan Province as an example to analyze the health of the innovation ecosystem in 2016, it also shows that their health was at a medium level. Based on the conclusions, it finally proposes corresponding countermeasures.