Abstract: R&D is the power resources for the sustainable development and transformation and upgrading of food processing industry.It has played an indispensable role in Taiwan′s food processing industry including growing,developing,maturity and transformation and upgrading.In this study,the status,characteristics and problems of sci-tech organizing system,R&D system and sci-tech investing system between Fujian and Taiwan were comparatively analyzed,and several suggestions were put forward for the sci-tech supporting system construction of food processing industry in Fujian and the sci-tech cooperation of food processing industry between Taiwan and Fujian on the basis of the succeed example in Taiwan.