The partnership between the HongKong Special Administrative Region and Guangdong Province in the field of science and technology has made a profound impact on the industrial and economic development of the two places，and has become a model for cooperation between HongKong and the Mainland. Based on the policy texts and statistical data of the science and technology cooperation mechanism between Guangdong and HongKong，this paper conducts a qualitative and quantitative analysis of the overall characteristics and regional division of labor of the science and technology cooperation mechanism between Guangdong and HongKong from the aspects of the development process of the cooperation mechanism，key cooperation areas and allocation of investment funds. The study found that the cooperation mechanism between Guangdong and HongKong is closely linked，with mutual communication and the continuously expanding coverage. In addition，the key areas and scopes of Guangdong-HongKong cooperation has also been analyzed. Based on this，the thesis proposed to build a common system of innovation and a platform base for science and technology cooperation between Guangdong and HongKong，to study in depth the reform of the cooperation mechanism between Guangdong and HongKong，and to provide more convenient entry and exit procedures，Increase the financial input of cooperation between universities and scientific research institutions in the two places，strengthen cooperation in intellectual property work related to cooperation between the two places，promote the flow of talents between Guangdong and Hong Kong，and simplify the approval procedures for the movement of scientific research personnel between the two places.