Developing patent intensive industries is an important strategy to promote industrial competitive advantage. Due to unbalanced development of economy and differences in leading industry of different regions, regional patent intensive industries are still faced with problems of mismatch between technology input and output, inactive technical transformation investment market and other problems, so it is urgent to do some researches on innovation efficiency evaluation and promotion path. Based on construction of regional patent intensive industries and from the perspective of innovation value chain, the paper divides innovation processes into three stages，including science and technology output, commodity output and value output, and studies by using DEA to differences in innovation efficiency of regional patent intensive industries and non-patent intensive industries at different stages. The paper indicates that innovation efficiency of regional patent intensive industries are better than non-patent intensive industries, but they are not DEA effective in every stages, and innovation input and output for some of the industries do not match and the input redundancy of these industries are serious in the stages of commodity output and value output. Then the paper puts forward the promotion path for innovation efficiency on regional patent intensive industries, and some countermeasures are suggested to promote industrial development.