Abstract: [Abstract]After joining World Trade Organization（WTO）， the Chinese government carried out pharmaceutical data protection under the TRIPS agreement， but there are still some deficiencies in the pharmaceutical data protection system of China. The rapid progress in the pharmaceutical industry of Japan was tightly related to the implement of pharmaceutical industry related polices， the re-investigation policy of post-marketing drugs in Japan not only played an important role in stimulating the initiatives of drug research companies， but also effectively weakened the side effects of the data protection system. By comparative study on pharmaceutical data protection system of China and Japan， this paper aims to find out the shortcomings existing in the process of the pharmaceutical data protection in China and provide some feasible suggestion for the further improvement of Chinese pharmaceutical data protection system.