As one of the important forces promoting the development of the marine economy, the marine biomedical industry (MBI) shows typical knowledge and technology-intensive characteristics. It is of great significance to explore the industrial innovation dynamic mechanism for breaking through the bottleneck of innovative development as well as achieving high-quality development. This paper constructed a system dynamics model for scientific and technological innovation (STI) in the MBI and then explored the dynamic mechanism of STI in the industry through simulation. The study found that, in the innovation environment subsystem, the two factors of the intellectual property protection intensity and the government’s scientific research funding input had the most significant positive driving effects on STI of the MBI; the promotion of government education funding input showed a significant strengthening trend over time, while the marine environmental regulation intensity had comparatively little effect on the level of STI. In the subsystem of innovation input, both innovation funding input and innovation personnel input were the direct driving forces for the improvement of the STI level. And enterprises played a dominant role in STI because the STI level of the MBI was more sensitive to the changes in enterprise innovation input. Compared with the individual factor input, the synergistic promotion effect of multiple factors is more significant. In addition, it was found that there was a low conversion rate of scientific research achievements in China’s MBI by analyzing the influence of various factors changing on technological output and economic output. Based on the research results, this paper puts forward corresponding policy suggestions in order to provide theoretical support and a practical basis for promoting the technological innovation level of China’s MBI as well as references for other countries.