Architecture and microanalysis of electrochemical energy storage and conversion materials has been currently a research focus. On the basis of the progress of our research, we have summarized several methods for clarification of surface morphology, structure and architecture chemistry by using advanced electron microscopy. They cover from scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to energy dispersive X-ray spectroscopy (EDS) and electron energy loss spectroscopy (EELS). The application, progress and advantages of electron microscopy in electrochemical energy storage and conversion materials are fully introduced, and the characteristics of different electron microscopy techniques and their applications in electrochemical energy system are also discussed. Finally, the future directions of advanced electron microscopy and analysis routes of electrochemical energy storage and conversion materials is proposed. Thus, it enables more insightful and accurate microanalysis of materials, searching for optimum preparation process and in turn provide guidance for fully improving electrochemical performances.