In order to analyze the patent development of bio pharmaceutical industry in Yunnan Province, hierarchical clustering analysis of patent data of biological medicine in Yunnan province from 1997 to 2016 was carried out in the patent database of the State Intellectual Property Office, taking the patent application quantity, authorization quantity, growth rate and efficiency are the hierarchical cluster variables, give the results of cluster analysis ,development trend of biotechnology industry patents in Yunnan Province in recent 20 years, key technical areas and high yield applicants. The clustering results are in good agreement with the overall development of the biomedical industry in Yunnan Province, and the future prospect is optimistic.