Energy management for energy harvesting-based embedded systems (EHES) is an emerging field, which aims to collect renewable energy from the environment to power an embedded system. In this work, we use the systematic mapping method to study the relevant literature, with the objective of exploring and analysing the state of the art in energy management for EHES, as well as to provide assistance for subsequent literature reviews. To this end, we conducted extensive searches to find articles related to energy harvesting, embedded systems, energy consumption, and energy management. We searched for papers from January 2005 to July 2019 from three mainstream databases, ACM, IEEE Xplore, and Web of Science, and found more than 3000 papers about EHES. Finally, we selected 142 eligible papers. We have completed the system mapping research from five aspects, namely, (1) research type (validation research, evaluation research, solution proposal, philosophical paper, opinion, and experience), (2) research goals (application or theory), (3) application scenarios, (4) tools or methods, and (5) paper distribution, such as publication year and authors’ nationality. The results showed that the major research type of the EHES papers is validation research, accounting for 65%, which indicated research is still in the theoretical stage and many researchers focus on how to improve the efficiency of harvesting energy, develop a reasonable energy supply plan, and adapt EHES for real-world requirements. Furthermore, this work reviews the tools used for EHES. As the future development direction, it is indispensable to provide tools to EHES for research, testing, development, and so on. The results of our analysis provide significant contributions to understanding the existing knowledge and highlighting potential future research opportunities in the EHES field.