Objective To comparatively analyze the functions of PubMed and Embase in searching evidence from EBM. Methods The functions of PubMed and Embase in searching evidence from EBN were compared in aspects of searching methods,searching process,data structure and searching results. Results Embase could provide more visualized and modularized searching methods,more advantages of searching evidence from EBM and more simplified searching process than PubMed. The searching framework of PubMed was more effectively fixed than that of Embase. PubMed could search the evidence from EBM through its embedded filter. The indexing method of PubMed was more standardized and the searching noise of PubMed was less than those of Embase.Conclusion PubMed and Embase are the highly used databases in biomedical field with their own characteristics and can thus complement their mutual advantages.