In order to provide a reference and theoretical guidance of the evaluation of electronic medical record (EMR) and establishment of evaluation system in China, we applied a bibliometric analysis to assess the application of methodologies used at home and abroad, as well as to summarize the advantages and disadvantages of them. We systematically searched international medical databases of Ovid-MEDLINE, EBSCOhost, EI, EMBASE, PubMed, IEEE, and China's medical databases of CBM and CNKI between Jan.1997 and Dec.2012. We also reviewed the reference lists of articles for relevant articles. We selected some qualified papers according to the pre-established inclusion and exclusion criteria, and did information extraction and analysis to the papers. Eventually, 1 736 papers were obtained from online database and other 16 articles from manual retrieval. Thirty-five articles met the inclusion and exclusion criteria and were retrieved and assessed. In the evaluation of EMR, US counted for 54.28% in the leading place, and Canada and Japan stood side by side and ranked second with 8.58%, respectively. For the application of evaluation methodology, Information System Success Model, Technology Acceptance Model (TAM), Innovation Diffusion Model and Cost-Benefit Access Model were widely applied with 25%, 20%, 12.5% and 10%, respectively. In this paper, we summarize our study on the application of methodologies of EMR evaluation, which can provide a reference to EMR evaluation in China.