The building of the Economic Zone on the West Coast of Taiwan Straits, in which Fujian is a principal province, and the construction of a tourism area in this zone are key issues in the development strategies of mainland China. However, few researches have been conducted on the spatial structure of Fujian tourism system. With the application of the fractal theory, spatial analysis techniques of GIS and statistical methods, this paper analyzes coupling relationship of the spatial pairs in Fujian' tourism destination systems, including tourism attraction subsystem, tourism city subsystem and tourism transport subsystem. The study shows that coupling relationship of the A-C spatial pairs in Fuzhou is in the best situation, implying that the spatial structure of Fuzhou is most compact. And Putian ranks the second position regarding compactness. As far as coupling extent of A-R spatial pairs is concerned, cities including Putian, Zhangzhou and Quanzhou are highest, is following Fuzhou, Wuyishan and Sanming. It should be noted that although the tourist attractions system, which is centered around Xiamen, is most compact in spatial structure, but its coupling relationship of the A-R spatial pairs is not the best. In coastal areas, coupling relationship of the C-R spatial pairs is in general good situateion. In particular, Fuzhou is the best in the condition of C-R spatial matching, following by Putian, Zhangzhou and Sanming. The coupling extent of the C-R spatial pairs in Wuyishan is even lower than Sanming. In conclusion, this study demonstrates that the fractal calculated results can objectively reflect mathematical relationships between various subsystems, and that the feasibility of applying fractal theory and method to researching into spatial structure of tourist destination system is obvious. By the study, the authors put forward some specific suggestions about constructing the North and South destination subsystems in Fujian.