Innovation resources have become the core competence of industries in the new era of economic development. It has become the focus of attention how to use the innovation resources effectively to serve the development of industrial clusters in the regions, and to bring more economic and social benefits. Due to low innovation resources efficiency, many industries confronted with the bottleneck of development. Based on the methodology of Data Envelopment Analysis (DEA) and Malmquist index, the concepts, as well as the approaches and models, of optimizing innovation resources efficiency for key industries in China are set up in the article. The results show that only three industries are efficient. The inefficiency of other industries is mainly due to poor technology efficiency. The M index results also show that trends of innovation resource efficiency are in accordance with that of economic environment. Emerging industries are growing rapidly with high efficiencies due to technological progress and advanced technology.