This study aims to explore the effect of innovation institution on spatial transfer of energy industry in Jiangsu, China. We focus on the disparity of innovation and energy industry, and analyze the spatial transfer difference in different types of energy industry, rather than view energy industry as a whole. The study demonstrates the spatial change of energy industry at regional level and maps the spatial pattern at city level. The study chooses intellectual property rights (IPRs) protection intensity, authorization patents and local research and development (R&D) investment as the proxy of innovation. Using official data and employing panel fixed-effect model at city-industry level, we conclude (a) innovation abilities significantly influence the spatial transfer of energy industry in Jiangsu. Especially, due to the different time, IPRs protection, patent counts, and R&D investment have different effects on different regions in Jiangsu; (b) 2010 is an important turning point for energy industry development in Jiangsu, and after 2010, the energy industry begins to shift to the middle and northern Jiangsu, whereas the spatial pattern of energy industry in coastal cities is basically unchanged; (c) there is a great difference between the regions in Jiangsu Province, and industrial upgrading has not been achieved in northern Jiangsu.