The new national system research model is an important means to promote the key core technology research and enhance the ability of independent innovation. Through the reform and innovation of the province"s science and technology plan project management system, Guangdong has explored the construction of a multi-agent, multi factor, whole chain key technology research mode of the whole country, and has formed some typical practices and experiences for reference in the formulation of scientific and technological innovation policies, the organization and Implementation of scientific and technological projects, the management and service of scientific and technological projects, and the overall allocation of scientific and technological innovation resources To form an important leading and exemplary role in the whole country. However, there are still some aspects to be improved in the new situation, new tasks and new requirements of the construction of the international science and technology innovation center in Guangdong, Hong Kong and Macao Bay area. For example, how to deal with the relationship between government and market, input and output, R D and Application, consolidation and dynamics, and enhance the situational adaptability and innovation performance of the model? Finally, some countermeasures and suggestions are put forward.