The key measure to solve the collaborative innovation of science and technology in the Guangdong-Hong Kong-Macao Greater Bay Area（GBA）is to establish and improve a set of institutional mechanisms suitable for the development of innovation in the GBA. Judging from the practical experience of scientific and technological innovation systems in the San Francisco Bay Area，Tokyo Bay Area and New York Bay Area，we can see that a sound innovative talent flow and training system，a sound scientific and technological research and development and achievement transformation guarantee system，and a sound “government-industry-university-research” scientific and technological innovation. The system and a strong government and intermediary regulation and support system are key elements to stably promote the improvement of regional scientific and technological innovation capabilities. The successful experience of the science and technology innovation systems in the three major international bay areas has important reference and reference significance for the coordinated development of science and technology innovation in the GBA.