The Rapid Autopsy Program (RAP) is a valuable procedure for studying human biology and diseases such as cancer. However, implementing the RAP in Japan necessitates a thorough understanding of concepts such as good death and the integration of sociocultural aspects. By revising perceptions of organ donation on social media, we bring attention to the challenges associated with implementing new medical research procedures such as the RAP. This study aims to examine YouTube and Twitter/X to identify stakeholders, evaluate the quality of organ donation communication, and analyze sociocultural aspects associated with organ donation. Based on our findings, we propose recommendations for the implementation of new medical research procedures. Using the term "" (organ donation), we collected data from YouTube and Twitter/X, categorizing them into 5 dimensions: time, individuality, place, activity, and relationships. We utilized a scale to evaluate the quality of organ donation information and categorized YouTube videos into 3 groups to analyze their differences using statistical methods. Additionally, we conducted a text-based analysis to explore narratives associated with organ donation. Most YouTube videos were uploaded in 2021 (189/638, 29.6%) and 2022 (165/638, 25.9%), while tweets about organ donation peaked between 2019 and 2022. Citizens (184/770, 23.9%), media (170/770, 22.0%), and unknown actors (121/770, 15.7%) were the primary uploaders of videos on organ donation. In a sample of average retweeted and liked tweets, citizens accounted for the majority of identified users (64/91, 70%, and 65/95, 68%, respectively). Regarding Japanese regions, there were numerous information videos about organ donation in Hokkaido (F2.46,147.74=-5.28, P=.005) and Kyushu and Okinawa (F2.46,147.74=-5.28, P=.005). On Twitter/X, Japan and China were the most frequently mentioned countries in relation to organ donation discussions. Information videos often focused on themes such as borrowed life and calls to register as donors, whereas videos categorized as no information and misinformation frequently included accusations of organ trafficking, often propagated by Chinese-American media. Tweets primarily centered around statements of donation intention and discussions about family consent. The majority of video hyperlinks directed users to YouTube and Twitter/X platforms, while Twitter/X hyperlinks predominantly led to news reports from Japanese media outlets. There is significant potential to implement new medical research procedures such as the RAP in Japan. Recommendations include conceptualizing research data as borrowed data, implementing horizontally diversified management of donation programs, and addressing issues related to science misinformation and popular culture trends.