In recent years, popular science short videos have shown a prosperous trend, but they have also encountered various issues in content creation. This study selects 63 popular science short videos released by Bilibili uploader "Bi Dao THU" from October 2019 to May 2021 as research samples. Drawing on the three-level framework theory and employing data analysis, content analysis, and user behavior analysis, this study focuses on exploring the optimization strategies in content creation. It addresses the main problems discovered in the research, such as the significant influence of commercial factors on objective expression and the relatively limited variety in presentation styles. From the perspectives of work quality and effectiveness evaluation, as well as the integration of theory and practice, the study proposes four pathways for improving and enhancing the quality of popular science short videos: balancing commercial and content logics, exploring multidimensional presentation styles, establishing brands and brand matrices, and strengthening a sense of responsibility.