Promoting the development of an innovative economy is an important part of China's current economic restructuring. Based on the analysis of the existing research results, the development of emerging industries need to construct a theoretical framework for policy intervention, and through the macro analysis of the strategic emerging industries that existing policies are effective, and find that the effectiveness is very limited. In further study, the bio pharmaceutical industry and new energy automotive industry listed companies as the research object, made a micro analysis on the fiscal policy role in its development, the policy effect due to the heterogeneity found industry presents heterogeneity, so as to find out the cause of the shortcomings of the current policy effectiveness. Accordingly, the industrial policy intervention should focus on the heterogeneity of the industry, further from the four aspects of industrial structure policy, industrial technology policy, industrial organization policy, regional industrial policy put forward policies to promote the development of emerging industry optimization suggestions.