This paper reviews the measuring method of industrial structure similarity, the changing trajectory and causal analysis of China regional structural similarity in recent years. This research shows that MKI completely coincides with SSI. The industrial structure similarity in China has first decreased, and then increased, at last with a downward trend in recent years. Empirically the paper analyzes the influence factors of manufacturing structural similarity, and the result shows that the government behavior has a great important influence on regional manufacturing structural similarity; Manufacturing structural similarity is negatively related to the following difference of factor between regions: resource, transportation costs, local government protection, level of economic development; Before one period lag, difference between government direct investment have the positive correlation with manufacturing structural similarity. Finally the paper puts forward relevant policy recommendations based on the changing trajectory of structural similarity and the conclusion of empirical analysis.