This study is to discuss the effectiveness evaluation of cardiovascular drugs based on CYP2C9 target protein. Multilevel fuzzy comprehensive evaluation method was taken to evaluate the individualized medication effectiveness for cardiovascular drug under the function of CYP2P9 target protein. Then, it was established for the index system to affect drug efficacy and index weight was settled. This index system was applied on the study of valsartan drugs to evaluate the drug efficacy rate of sample. Results corresponded with the actual drug treatment, and received better verification. The beneficial exploration was performed for the effectiveness evaluation of individualized administration.