The focus of structural reform is to fully promote labor mobility on the basis of market allocation through changes, adjustments and optimization of economic structure, so that labor in low-efficiency departments can fully flow to high-efficiency departments, thus to stimulate the production enthusiasm of workers and to promote the growth of labor productivity. Therefore, the structural efficiency difference model between the two departments theoretically analyzes the impact of labor mobility between high-efficiency departments and low-efficiency departments in stimulating the enthusiasm of workers and improving labor productivity. On this basis, the annual time series data of the urban and rural structure, industrial structure, ownership structure and regional structure from 1978 to 2017 are used to analyze their respective impacts on changes of labor productivity. The measurement results show that among the effects of various structural changes on labor productivity, urbanization, moderate equilibrium of regional economy, accelerated development of conditional regions, marketization and optimization of industrial structure are in order of magnitude. Therefore, it is necessary to improve labor productivity by effectively promoting urbanization, moderately leading economic development in developed regions, marketization and high industrial structure.