Background <p>Medical mentors’ innovation competence, which has not yet been effectively evaluated, is crucial for cultivating talent in the medical field. In this study, we aim to develop a new tool for assessing medical mentors’ innovation competence.</p> Methods <p>Thirteen experts were interviewed and consulted to identify items indicating innovation competence. These items were used to prepare a questionnaire for the subsequent cross-sectional survey. Finally, the innovation competence instrument was developed and verified through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) using data from 1892 mentors and postgraduates at 9 Chinese universities.</p> Results <p>Five dimensions— “mentoring and teamwork”, “supportive action”, “scientific research”, “professional ethics and spirit” and “educational reform”—including 21 items—were developed and verified. The instrument explained 68.66% of the total variance, and it exhibited good reliability and validity as well as a good fit to the data.</p> Conclusions <p>The instrument provides a new theoretical framework for innovation competence in postgraduate education, and it can be used to assess the innovation competence of mentors to guide them to better prepare for mentoring medical postgraduate students. Additionally, the results suggested that mentors should focus on “mentoring and teamwork”, especially collaboration with postgraduates, to improve innovation competence.</p>