Abstract: The industrial structure is an important part of the economic structure. The optimization of industrial structure is the important condition to improve the economic & social benefits and promote the transformation of economic development pattern. It is also the basic guarantee to improve the supply structure, to achieve a high level of balance between supply and demand, and to better meet the needs of production and life. Based on the gross domestic product of Fujian and its industrial structure, the three industrial structure deviation, the comparative labor productivity and the rate of contribution to economic growth were analyzed in this paper. Then, by using the ShiftShare Analysis, the changes of Fujian’s industrial structure were analyzed in depth, and the existing problems in it were explored. Last, the countermeasures for the optimization of industrial structure in Fujian were put forward.