As the global transportation sector accelerates toward net-zero targets, the rapid deployment of alternative fuels like hydrogen, ammonia, and batteries introduces complex and novel safety challenges. This study systematically maps the intellectual structure of safety and risk research on zero-emission transportation systems to evaluate field maturity and identify critical knowledge gaps. We conducted a comprehensive bibliometric analysis of 151 core publications retrieved from the Web of Science from 2000 to 2025. By integrating quantitative performance analysis with qualitative science mapping techniques, the results identify that the domain is nascent and rapidly expanding, and a distinct inflection in publication occurred in 2020. However, science mapping reveals a fragmented intellectual structure. Among the four identified research clusters, two dominant streams emerge as the primary drivers of the field. The first is a “motor theme” focused on lithium-ion battery reliability and thermal runaway, while the second is a “basic theme” focused on hydrogen dispersion and toxicity risks. The analysis exposes a blind spot regarding the lack of cross-modal research addressing the physical safety interactions between different fuel systems operating in the shared infrastructure. Finally, this study proposes a future research agenda focusing on gathering real-world accident data and using system-theoretic approaches to manage integrated alternative fuel risks.