With the regional integration of Yangtze River Delta officially rising as a national strategy, the cooperation between innovation subjects in Shanghai, Jiangsu, Zhejiang and Anhui is increasingly active and closer. Strengthening trans-regional joint research on key technologies in the Yangtze River Delta is helpful to gather the superior strength of enterprises, universities and research institutions, improve the efficiency of scientific and technological resource allocation, and enhance the overall scientific and technological competitiveness of the region. The innovation collaboration development across regions in the Yangtze river delta key generic technology joint research problem has carried out in-depth research, the current situation is studied, analyzes the institutional barriers and mechanisms hindering the innovation collaboration in the Yangtze River Delta region are analyzed, and some policy suggestions are put forward to promote the common technology joint research in the Yangtze River Delta region.