Abstract: In the perspective of competitiveness and complementarity, the trade structures and trade relations on the trade of agricultural products in both sides of the Taiwan Straits were analyzed. The trade competitiveness index(TCI) was using to measure and compare the competitive advantage of agricultural products trade between Mainland and Taiwan, and the intraindustry trade index(GLI) was applied to measure the complementary degree of agricultural products trade between Mainland and Taiwan. The results showed that both sides of the Taiwan Straits should further strengthen agricultural cooperation and communication, promote agricultural twoway investment, reinforce the communication and cooperation of agricultural products inspection and quarantine, and take Fujian and Taiwan as the test point to promote development of agricultural integration.