Pharmaceutical companies may have incentives to exaggerate the therapeutic effects of their developed products during the clinical stage, which endangers the health of patients. To increase transparency in clinical practice, the NIH established ClinicalTrials.gov in 2000, which indicates a significant impact on medicine. However, little evidence shows how ClinicalTrials.gov affects medical enterprises innovation. By identifying the patent application activities through USPTO, Pubmed, and Compustat, we used coherent DID to prove the impact of ClinicalTrials.gov on innovation. We found that the emergence of ClinicalTrials.gov reduced the number of patent applications and led to a shift in RD directions. This effect can also be moderated depending on firm size, probably because small companies are more incentivized to manipulate data. Hence, we suggest agencies could consider wide-ranging influences when formulating open science policies.