The agricultural cooperation between Fujian and Taiwan as a whole presents thorough development trend, the basic realization of the agricultural industry of mutual benefit and reciprocity, to achieve development in both economics and policy. But the agricultural cooperation between Fujian and Taiwan still has some problems:lack of sound management system, cooperative innovation capacity is obviously insufficient; the lack of perfect investment environment, industry docking capacity is obviously insufficient; lack of effective investment in science and technology, agricultural exchanges and cooperation is obviously insufficient; lack of scientific industry planning, balanced industrial development ability. The construction of innovation perspective of agricultural cooperation between Fujian and Taiwan should be based on the mode of cooperation. By complementarity, mutual benefit, the principle of mutual benefit of cooperative security system;establish the sharing cooperation mode in agricultural technical resources and research; form closer cross-strait cooperation mode; make innovation of rural industry development in modern equilibrium way.