Abstract:the Guangdong-Hong Kong-Macao Greater Bay Area has become the bridgehead of China"s innovation-driven development, helping China speed up the improvement of scientific and technological innovation capacity. This paper selects data related to the technological innovation capacity of "9+2" cities in the guangdong-hong kong-macao greater bay area over the years to build a panel data set. In order to further analyze the differences in scientific and technological innovation capability among bay area regions, the bay area is divided into West bay, Central bay, East bay and Hong Kong and Macao bay. Based on the analysis theories and methods of spatial difference, spatial autocorrelation and spatial measurement, and with the help of GeoDa, ArcGIS and Stata data analysis software, the spatial structure evolution and its influencing factors of the scientific and technological innovation capacity of guangdong-hong kong-macao greater bay area were deeply studied.