In order to promote the development and application of medical data mining in China, we made a comparative analysis of the similarities and differences between the domestic and abroad researches based on quantitatively and qualitatively analyzing the articles about medical data mining included in CNKI and Web of ScienceTM from 1998 to 2016 using bibliometrics and knowledge mapping from the aspects of number of articles, core authors and research institutions, and the hotspot and research frontier.