The characteristics of a complex system are presented in the innovation activities of humankind.This paper summarized the recent findings of applying the complex system theory to study the innovation processes,with a special focus on the origin,structure and evolution of innovations.We noticed that many models and concepts used in the study of innovation systems are adopted from the biology systems,yet the social system and the biology system apparently are at very different levels of complexities.Therefore,this paper argues that while trying to explore the general rules that may apply to all complex systems,one should also keep mind open for the unique rules that apply only to the social systems,including the innovation activities.In addition,due to its interdisciplinary nature,it would be more fruitful for scholars from different academic backgrounds to join forces in the study of the innovation process under the complex system paradigm.