The paper puts forward the method for evaluation on the scientific influence of institution based on PageRank algorithm, configures the initial weight of each institution based on the problems of dividing equally the webpage weight number in the classical PageRank algorithm and cited frequency of the application chapter, constructs the network matrix cited by institution through the citation situation of medical SCI papers published by partial colleges and universities in 2015, respectively calculates the PageRank values of institution when self-citation is excluded or included, and conducts comparative analysis on the sequence of cited frequency indicators of the institution as well as H index. This method can be used to evaluate scientific influence of institution from two dimensions of quality and quantity.