This study uses Regional Input-Output analysis by Miller and Blair (2009) and the 96 sectors Cross-straits Regional Input-Output table compiled by Lin (2013) to analyze the direct and indirect impact of agricultural products in related industries and the overall economics. The study simulates the following three scenarios. Firstly, the amount of Taiwan's agricultural exports to China and the amount of net exports during 2009-2012 to investigate the economic impact in Taiwan which includes ECFA and the substitution effect. Secondly, Taiwan's earnings amount of agricultural exports due to the real effect by tax reduction after the implementation of the ECFA. This effect only includes the tax reduction effect because Taiwan does not offer any early closing deal in agricultural goods in ECFA and still controls the 830 goods import from China and no tariff reduction in 1,415 commodities. Thirdly, the study estimate the real impact on the substitution between Cross-strait commodities if the removal of the ban on Chinese goods into Taiwan in the future. Compare of three scenarios empirical results comprehensively, this study find there will be a positive benefit in total output effect of Taiwan's exports to China and profitable due to tariff reduction although the implementation of ECFA will generate negative results in net exports. There has negative overall effect if opening of China's agricultural imports from Taiwan in the future. This study also found in fishery and other food exports and the net exports of output results are high, and the total output due to the effect of the tariff reduction benefit is also high, indicating that for the two departments in Taiwan, the Cross-strait agricultural trade will benefits department, except that if the future opening of China's agricultural imports to Taiwan, in considering the Chinese imports of Taiwan under the effect of product substitution, then the three sectors will be reduced mainly by the impact of the opening.