Clustering is an important mode and main path of strategic emerging industries development. According to the problems in inadequate industrial technology reserves and lagging market cultivation in the process of China’s strategic emerging industrial clusters development, this paper reviews the related supporting theories of strategic emerging industrial clusters cooperative development from the theoretical perspective of industry cluster, strategic emerging industry cluster, industrial clusters cooperative development as well as co-development of ecology, explores the general law of the existing theories and their shortcomings, and then analyzes the future research focus and direction. The future research focus will be the ecological niche theory grafting and then integrated into the industrial cluster theory based on the combining of the characteristics of China’s strategic emerging industry cluster development. Finally, the paper analyzes the mechanism of the cooperative transition of “technology nichemarket niche” in strategic emerging industrial cluster, and puts forward relevant mechanisms, policies, etc..