In order to evaluate and analyze the relative strength of the disciplines at the first level of Medical University and the rationality of the subject structure, the output of academic papers in the first-level disciplines of Wenzhou Medical University was compared with similar institutions at home and abroad by INCITES database. The results show that the number of papers at the main level of Wenzhou Medical University is higher than the average of similar institutions, but the academic influence of the papers needs to be improved and the subject structure needs to be optimized. Wenzhou Medical University should maintain a large academic volume, with clinical medicine first-level disciplines as the core, strengthen main medical first-level disciplines, further optimize the subject structure, and improve the overall academic level of the University.