The combination of technological innovation and financial ecology is an important foundation and prerequisite for high-quality social and economic development. As one of the national development strategic highlands and one of the regions with high economic vitality, the Guangdong-Hong Kong-Macao Greater Bay Area has made achievements in promoting scientific-technological innovation, financial development and industrial integration. Based on the panel data of scientific-technological innovation and financial development of cities in the Greater Bay Area from 2009 to 2018, we constructed the evaluation system of scientific and technological innovation and financial development, and measured the coupling degree of sci-tech finance in the area, and analyzed its influencing factors by adopting the panel model regression with the consideration of government investment in science and technology, financial efficiency and scale of high-tech enterprises and so on, and used the Moran's I index of coupling coordination degree of technology and finance to estimate the space spillover effects in the study area. The results indicate that the public technology finance and market technology finance in the Greater Bay Area have shown a rapid development trend. The investment in public technology finance continues to increase, and market technology finance forms are constantly innovating, and the institutional system is becoming perfect. The sci-tech finance coupling degree of cities in the area shows a trend of optimization with the leap of “severe disorder-moderate disorder-almost disorder” year by year, while there are some significant spatial differences among regions, especially for the cities of Shenzhen, Guangzhou and Hong Kong with the highest degree of coupling coordination and the cities of Zhuhai, Huizhou, Jiangmen with moderate disorder. The sci-tech finance coupling degree is positively affected by factors such as government investment in science and technology, financial efficiency, and high-tech development. However, the spatial spillover effect of the coupling degree of sci-tech finance in Guangdong province and Hong Kong is not obvious. Finally, we put forward some policy recommendations from the perspectives of government agencies, financial institutions, scientific and technological enterprises, and technology-finance service departments, in order to build the Greater Bay Area into a global international scientific and technological innovation center.