Abstract Since the surge of the cross-strait trade and investment in the 1990s, Taiwan and China have become major trading partners with each other. However, the persistent political conflicts across the Taiwan Strait have significantly influenced the trade flow of the two sides, and increasing close economic tie between the two has also generated profound effect on their political situation. The purpose of the paper is to empirically test the causal relationship between economic integration and political conflicts by using quarterly data from Taiwan and China pertaining to the 1996-2008 period. The estimation results show that there is a significant positive bi-lateral causality between Taiwanese firms’ investment in China and Taiwan’s export to China implying that foreign direct investment induced exports and exports attracted foreign direct investment, while the improvement in the cross-strait relations perceived by Taiwanese people has a positive causal effect on Chinese leaders’ political friendly response. These results imply that no causal relationship between economic tie and political tension, i.e., economic variables are separated from political factors. Taiwan’s restricted trade policy with political confrontation policy against China during the 1996-2008 period and the economic benefits through cross-strait industrial division of laborwere likely the major reasons causing the separation of economic tie and political conflicts between Taiwan and China.