Innovative drug R&D is one of the critical factors to enhance the core competitiveness of pharmaceutical industry，which plays a major role on acquiring social and economic benefits. Due to the characteristics of “high investment，long period and high-risk” drug innovation bears，the pharmaceutical company can be guided obviously by the government incentive and regulatory policies. Based on a comparative analysis on Chinese and Foreign Innovative Drug R&D Ability，this paper establishes a structure evaluation model to evaluate the implemented effectiveness of innovative policies. And then put forward some policy recommendations for the innovation drug research and development.