Abstract: Based on the utility patents approved by the US Patent and Trademark Office from 2008 to 2009, and by using multiple patent index, the overall innovation performance on both sides of the Taiwan Straits and the cooperative interaction of the cross-strait innovation members are examined. The research results show that: So far, Taiwan’s patent layout in America has been better than that of the Chinese mainland, but in recent years, the growth rate of the mainland’s patent ownership has exceeded Taiwan. From the perspective of patent layout, the cross-strait industrial technology research field and focus are basically consistent. For the cross-strait enterprises, especially large enterprises, they play an important role of innovation body in the innovation system, but the innovation knowledge interaction degree of the coast-strait patent research main body is low, and the multinational cooperative development is also very limited. Under the trend of globalization, in the face of open innovation ideas, the interaction between the cross-strait and international innovation or knowledge should be more active.