The economic and trade exchange between Taiwan and Fujian in real significance can be realized by that “Fujian has the products from Taiwan and that Taiwan has the products from Fujian”, and Intra-industry trade can embody this kind of economic and trade exchange relation. HS classification method is used to classify agricultural products into 24 chapters and 4 classes, and then marginal intra-industry trade index of total agri-product and each class of argi-product between Fujian and Taiwan from 1996 to 2009 is separately calculated. The results show that intra-industry trade level between Fujian and Taiwan is relatively low, however, its vertical intra-industry trade level is relatively high, and that the increment of its intra-industry trade mainly comes from vertical intra-industry trade. In order to further take advantage of “small trade” between Fujian and Taiwan and reduce quality disparity of agri-product between Fujian and Taiwan, Fujian should boost quality of agri-product, specifically meet the demand of Taiwan consumers, also bring traditional advantage into play and actively learn management mode of Taiwan agricultural production. 