With the rapid development of new media, Micro-video of Science Popularization is favored by the public and science popularization workers with its short, flat and fast features, and also brings about a strong impetus to the popularization of science. In order to effectively popularize scientific knowledge, it is imperative to design and produce suitable Micro-video of Science Popularization. How to design Micro-video of Science Popularization, and to make it a great vehicle for popularization of science is an important issue worth thinking. In this paper, the present situation of Micro-video design is investigated, and the related research of Micro-video of Science Popularization is carried out, meanwhile, the characteristics of classic Micro-video of Science Popularization at home and abroad are comparatively analyzed. Finally, some suggestions are made for the design of Micro-video of Science Popularization, providing some theoretical guidance for the design of Micro-video of Science Popularization, and to adding new and powerful channels for popularization of science.