In order to gain an in-depth understanding of the status quo of clinical medical scientific research competitiveness of independent medical universities , factor analysis is used based on the InCites database is used to analyze the scale of scientific research output and the influence of scientific research output from two dimensions. The clinical medical scientific research competitiveness of medical universities is objectively evaluated, and 27 universities is ranked in terms of clinical medical scientific research productivity, scientific research influence and scientific research competitiveness. The results show that the top three in clinical medical research productivity are Capital Medical University, Peking Union Medical College, and Nanjing Medical University, and the top three in scientific research influence are Guangdong Medical University, Harbin Medical University, and Guangzhou Medical University. The top three in terms of competitiveness are Peking Union Medical College, Capital Medical University, and Guangzhou Medical University. It is suggested that universities combine their own advantages and disadvantages to make targeted improvements to further enhance the scientific research competitiveness of clinical medical.