The popularization of health knowledge plays a crucial role in the transformation of the medical system from a treatment-oriented approach to a prevention-oriented approach that combines prevention and treatment. This study explores non-linear the common problems in the current popularization of health knowledge, such as high reading barriers, insufficient attractiveness, and difficulty in stimulating the public’s willingness to actively learn about health knowledge. This study proposes a visualization design method for health knowledge based on interactive narrative, and applies and evaluates the method using health knowledge related to headaches as an example. The results indicate that the design method has a significant positive impact on the popularization of health knowledge. It not only enhances the attractiveness of health knowledge popularization and strengthens users’ subjective learning willingness, but also effectively guides users to think deeply and better understand health knowledge.