In response to the evolving landscape of global technological competition and the pressing demands of national security, relying solely on conventional science and technology innovation organizational mechanisms may lead to systemic failures in achieving strategic technological breakthroughs, highlighting the urgent need for extraordinary mechanisms. Drawing on the theory of innovation system failures, this paper systematically examines the extraordinary science and technology innovation organizational mechanism under a national mission-oriented framework. It clarifies its conceptual boundaries, key characteristics, and its complementary relationship with conventional mechanisms, while revealing China’s institutional advantages in resource coordination and allocation, internal market integration, production and supply capabilities, and authentic application scenarios. Based on this analysis, the paper argues that the effective operation of extraordinary mechanisms requires balancing three fundamental relationships: technological security and technological openness, a proactive government and an efficient market, and the division of labor and coordination among key innovation actors. The dynamic coordination of these relationships enables extraordinary science and technology innovation organizational mechanisms to achieve precise resource mobilization and integrate exploratory innovation with mission-oriented technological breakthroughs, thereby fostering an efficient innovation ecosystem and providing robust organizational support for the development of a modern industrial system and the advancement of Chinese modernization.