Since the last two decades, microgrid, as one typical structure in smart grid framework, has been receiving increasing attention in the world. Meanwhile, fuel cell (FC), as one promising power source, has redrawn the attention of both academia and industry since the beginning of 21th century. Some encouraging achievements in FC technology have been realized thanks to the efforts taken in the last years. Due to this, it is seen that FC, as a clean and efficient energy source, is penetrating into different fields. Among the applications, integrating FCs into microgrids has shown interesting advantages on improving the performance of microgrids and promoting the use of the hydrogen energy. Some ongoing projects have shown that FCs of different power scales can be integrated into microgrids smartly and in different manners. Along with the advantages carried by the combination of the two technologies, many challenges lying on multiple domains are faced in the process. The challenges can be from the FC, the microgrid, and the integration of these two technologies. In this review paper, the advantages of integrating FCs into microgrids are summarized after recalling the knowledge background of FC. The challenges and ongoing researches on FCs and FCs based microgrids are then reviewed. Based on the analysis, the research directions are then extracted in view of the challenges.