The lifespan and stability of power supply are the most critical issues for implantable biomedical devices (IMDs). Extracting energy from the ambient sources or human body therefore attracts a lot of attentions for in vivo therapies. Micro-electromechanical systems (MEMSs) based energy harvesters are expected to be one of the potential solutions to supply electrical power to IMDs owing to its tiny size, light weight and recharge-free attributes. However, the performance of the micro-energy harvester for implantable biomedical applications is limited by many inherent congenital factors. In this paper, three main topics are comprehensively studied and discussed. At first, the energy sources to be scavenged from human body are particularly investigated and characterized. Secondly, the operation principle and key bottlenecks of the currently available MEMS-based energy harvesters are reviewed and presented. Finally, the performance, frequency tuning methods and biocompatibility of micro-energy harvester are evaluated and summarized.