The labor flow promotes the industrial structure evolution, thereby affecting the growth of productivity. In the western industrialized countries, improvement in labor productivity has become an important source of economic growth. On the basis of analyzing changes of the industrial structure, changes of the structure of labor factor, changes of labor productivity and the growth rate in Guangdong Province in different periods, we use shift-share method to analyze the labor productivity effect of industrial structure in Guangdong Province, and put forward the following recommendations for the adjustment of industrial structure in Guangdong Province: (i) The adjustment of industrial structure should promote the reasonable and effective flow of labor between industries; (ii) Accelerating the optimization of the industrial structure is conducive to economic growth and improvement in labor productivity; (iii) In addition to structural optimization, the improvement in labor productivity should also focus on the improvement in intra-industry technology.