Popular science journals can conveniently and effectively communicate complex scientific knowledge with the help of short videos, offering unique advantages of enhancing the efficiency of information conveyance and improving readers' understanding. This study examines short videos of popular science journals by adopting the case study method to analyze the visual rhetoric of the selected short videos of excellent popular science journals. The findings indicate that in content presentation, elaboration and case presentation are the dominant paradigms in short videos of popular science journals, while there is an obvious disconnect in data visualization presentation. The principles of scientific knowledge, often abstract and complex, require clear visual representation through graphs, charts and other means. Without such visualization, it is difficult for ordinary viewers to grasp core ideas or discover the laws hidden behind the data. Regarding narrative design, although the technical advantages of dynamic graphics and special effects are fully released, the immersive design of interface architecture and interactive elements fail to establish a comprehensive narrative system. The lack of interactive design can easily block the bidirectional communication mechanism of science communication. The absence of interactive functions in short videos, such as click-triggered dynamic buttons and adjustable experiments, diminished the audience's willingness to actively explore the principles of science. Regarding sensory guidance, metaphorical and symbolic symbols build a three-dimensional cognitive network, while the lack of emotionally guided symbols leads to a significant cognitive empathy gap. The presentation of short videos was originally intended to bring scientific knowledge closer to the audience. However, if the audience lacks emotional resonance in the process, the mechanical mode of knowledge instillation can neither arouse the audience's curiosity in scientific exploration nor establish a meaningful connection between scientific topics and individual life, which ultimately leads to the reduction of scientific communication to a one-way delivery of information rather than meaningful transmission of ideas and values. Based on these findings, this paper recommends first strengthening content presentation and logical structure, while enhancing visual appeal by translating the published knowledge. To address insufficient scientific and technological knowledge data visualization in content presentation, dynamic charts (such as line graphs, heat maps, 3D models) can be used to replace static charts, disassembling complex data into multi-layer infographics, thereby lowering the threshold of comprehension through step-by-step animation displays from macroscopic to microcosmic, and from holistic to localized, so as to enhance the visual attractiveness of the short videos of popular science journals. Second, the emotional resonance of narrative design should be strategically utilized to strengthen the empathetic connection between the content and the audience. Using engaging storytelling, scientific knowledge is integrated into the plot with emotional color, so that the audience can naturally accept scientific information while becoming immersed in the narrative experience. Third, it needs to optimize sensory guidance and digital narrative, and refine content to stimulate communication potential. Using vivid images, warm or inspiring color schemes, and infectious character expressions or actions, abstract scientific concepts can be made more relevant and easy to perceive.