Under the background of economic transition, the adjustment of industrial and spatial structure of Fujian Province should be carried out on three aspects. Firstly, to find chance from the industrial transition all over the world and establish development strategy of itself. Secondly, to find new growth spots from the new change on the politics and economic structure of relations between Taiwan Province and Chinese mainland and to restructure the spatial structure according to it. Thirdly, Fujian Province must find its advantage from local space and form harmonious integration with above two aspects, on the premise of coordinating interregional labor division. Among the three aspects, the relations of Taiwan Province and Chinese mainland is the core to control industrial and spatial structure adjustment. Relations between Taiwan and Chinese mainland are getting better and better, besides, Fujian has the special location predominance, which determines that the adjustment of industrial and spatial structure of Fujian Province must be established on the basis of interaction of Fujian and Taiwan provinces. As for industrial structure adjustment, core aims are to select key industrial departments and to optimize regional economic growth model. Rest on logic course of co-operative industries selection between Fujian and Taiwan provinces, there are three important contents of industrial departments selection: 1) Cluster of agriculture. It includes productive cooperation and the system cooperation on agriculture support and promotion, and the key is to develop highly efficient agriculture and spread advanced modern agriculture administration system. 2) The adjustment of manufacture department cluster includes IT, automobile and petrochemical industries. Scale structure and spatial structure should be adjusted at the same time. 3) The core departments of tertiary production cluster are finance, logistics and harbor serves. To achieve economic integration between two seashores of Taiwan Strait, spatial structure reorganization on the basis of interactive action between Taiwan and Fujian province will pass through five stages: 1) Stage of five urban economic regions; 2) Integrated incipience of urban economic regions; 3) Stage of Fuzhou and Xiamen economic circle; 4) Stage of coastal urban economic zone; 5) Stage of integrated economic area between Fujian and Taiwan provinces. On the basis of five urban economic regions at present, the prospective spatial structure after adjustment should become integrated open space after through the five stages of urban economic regional integration and establish space system which contains four parts: the space of flows, the transition space, local space and radiation space.