The China mainland and Taiwan Region can be complemented in many areas. As one of the most developed provinces in the east of China, Jiangsu is closer to Taiwan. The two areas also have many cooperation areas. The Analysis on the shifts of industrial structures of Jiangsu and Taiwan reveal a tendency that there exists a gap in the proportion of industrial structures, which offers an enormous possibility for their cooperation. To take advantage of this opportunity, Jiangsu needs to create favorable cooperative environment, accept Taiwan industrial shifts and establish reasonable industrial division to facilitate the economic development.