Abstract. With the development of medical information technology, the research and application of medical big data has become an important direction of data research. The semantic similarity evaluation between medical domain knowledge is an important part of the understanding of medical large data, which can effectively promote the processing, classification and structured processing of medical resources. In medical domain knowledge, the similarity calculation can improve the performance of information retrieval of medical resources and effectively promote the integration of heterogeneous clinical data. Based on the analysis of semantic similarity and semantic correlation algorithm and combined with the characteristics of medical psychology knowledge, the paper introduces the concept of weight value to simulate the characteristics of human psychological quantity, and gives the medical domain knowledge semantic similarity calculation method. Finally adding the semantic structure model with Oxford Centre for Tropical Forests(OCTF) similarity, constitute OCTF similarity calculation model based on the semantic, and formulas are given. By using Systematized Nomenclature of Medicine --Clinical Terms(SNOMED CT) as the input ontology, the accuracy and usability of the algorithm are verified by the evaluation standard of medical terminology.