National science and technology major projects strive to master a number of core key technologies related to international people′s livelihood and national security, and its core task is the development of strategic products with independent intellectual property rights. Full use of the intellectual property system can provide support for protecting scientific and technological innovation achievements, promoting the transfer and application of intellectual property, and cultivating and developing strategic emerging industries. To this end, the Ministry of Science and Technology and other four national ministries and commissions jointly formulated the Interim Provisions on the Management of Intellectual Property Rights for national science and technology major projects, which set clear requirements for intellectual property work in project application, project evaluation, contract signing, process management, and acceptance. However, the national science and technology major projects have the characteristics of many participants, a long research period and easy to be affected by the external environment and internal factors. It is a key scientific issue in the field of intellectual property to run the intellectual property cultivation management through the whole innovation chain of national science and technology major projects, realizing the dual effects of promoting innovation with intellectual property rights and the output of more intellectual property rights with innovation.Existing literature mostly focuses on the influencing factors, mechanisms and protection of intellectual property rights. Some scholars have conducted research on issues related to major national science and technology special intellectual property rights, but most of them focus on the ownership and distribution of intellectual property achievements, and there are few researches on the cultivation of major national science and technology special intellectual property rights. Taking into account the characteristics of national science and technology major projects, how to show the intellectual property incubation process in the entire innovation chain is particularly important, and it is necessary to thoroughly study its cultivation mechanism and evolution mechanism.Therefore, the paper first proposes a conceptual model of the intellectual property rights cultivation mechanism for national science and technology major projects under the innovation chain based on synergetics and system theory, and uses the identification of key elements in the intellectual property cultivation process as an entry point to the in-depth study of the coupling relationship of the entire innovation chain of national science and technology major projects with intellectual property cultivation stage. Secondly, through collecting relevant national policies and combining them with the major and special intellectual property rights cultivation process, theoretical elaboration is carried out to establish a theoretical basis for constructing the model. Thirdly, analyzing the internal factors and external environmental factors that affect the cultivation of major national science and technology special intellectual property rights, refines the key elements that affect the cultivation of intellectual property rights. On the basis of extracting key elements, this paper uses system dynamics to establish the causal circuit diagram and flow diagram of the intellectual property cultivation mechanism, and divides the intellectual property cultivation system into four subsystems: the technical standard formulation subsystem, patent cultivation subsystem, innovation revenue subsystem and external environmental impact effect subsystem, to analyze the intellectual property rights cultivation mechanism for the entire innovation. Finally, in response to major special intellectual property rights issues, some suggestions were made in this paper from five aspects strengthening government control, forming a technical standard system, promoting the industrialization of results, creating a good market environment, and exploring full-process management. This research is of great significance for designing an effective path for the cultivation of major scientific and technological special intellectual property rights, realizing precise government policies, and increasing the number of core independent intellectual property rights, thereby enhancing China′s independent innovation capabilities and breaking through foreign blockades on key core technologies.