Abstract: China's high-end product manufacturing and technological innovation are facing a prominent "neck" dilemma. Major scientific and technological projects under the background of the new national system are an important organization and implementation mechanism for breaking through the "neck" technology with Chinese characteristics and comparative advantages. Aiming at the research problem of "how to break through the technical dilemma of 'stuck neck' through major scientific and technological projects", this paper takes Beidou system, a major scientific and technological project, as the research object, and takes three "stuck neck" technologies of Beidou-1 system, on-board atomic clock and GNSS satellite navigation chip as embedded cases. The study found that major scientific and technological projects have strong situational inclusiveness in breaking through the "bottleneck". As an organization and implementation mode of a new national system, in the process of breaking through the "bottleneck", such as technology identification, innovation strategy selection, R & D investment, technology catch-up opportunity creation and technology industrialization, Through the effective organization and allocation of technological innovation resources and the innovation management system and operation mechanism, we can play a role in targeted technological innovation management.