Abstract:In the background of Guangdong implement the strategy of innovation driven development vigorously, it has an important practical significance and function to strengthen science and technology cooperation between Guangdong and Hong Kong, which can promote industrial transformation and upgrading, and enhance regional competitiveness. According to the evolution process, the science and technology cooperation between Guangdong and Hong Kong could be divided into three stages, which are spontaneous cooperation, policy guidance and comprehensive cooperation. Research shows that: In different stages, the internal driving force, mode of cooperation and cooperation content have great difference in science and technology cooperation between Guangdong and Hong Kong, which has developed from the initial extensive folk spontaneous cooperation to the comprehensive cooperation stage with government guidance and market allocation, and has made great progress in the innovation of science and technology system, the integration of innovation resources and industrial transformation and upgrading, but there are also some problems such as micro cooperation mechanism is not perfect, cooperation "channel" is not smooth, joint research ability is not strong and so on. Finally, puts forward some countermeasures and suggestions aiming at the existing problems.