Because of the rising trade protectionism and production costs in China, the demand of climbing high-value chain has prompted the transformation and upgrading of traditional industrial clusters to innovative industrial clusters. This article uses case analysis method to study the cases of China’s Zhongguancun Science Park and the Tongji Knowledge Economy Zone,to proposes two transformation paths from traditional industrial clusters to innovation clusters. It also pointed out the current problems of "university and research" and government policy in the cluster upgrade, and put forward suggestions on improving the cluster ecology through virtual clusters, establishing a good research atmosphere in university and playing a supporting role by government policies.