Currently, the unprecedented global changes are accelerating, and innovative government governance has become an important factor for countries to promote social progress and national development. The two-way coupling drive between government governance innovation and national identity complements each other and jointly promotes the development and progress of the country. By analyzing the logical path between government governance innovation and national identity, it can be found that China’s government governance innovation faces multiple governance challenges such as information transparency, cultural diversity, uneven economic development, and digital technology transformation. The Third Plenary Session of the 20th Central Committee of the Communist Party of China further clarified the need to continue improving and developing the socialist system with Chinese characteristics, and to promote the modernization of the national governance system and governance capacity. The modernization of government governance is an important part of the modernization of the national governance system and government governance is an important dimension for measuring the effectiveness of modernization in government governance. The driving mechanism for innovative government governance in the new era is diversified, covering policy and regulatory incentives, economic and financial incentives, cultural and educational promotion, and so on. The interaction between these mechanisms forms a dynamic system that promotes national identity, facilitating the construction and consolidation of national identity. By integrating these innovative mechanisms, the government can not only effectively address current governance challenges, but also lay a solid foundation for the country’s sustainable development from a longer-term perspective. The interactive relationship between government governance innovation and national identity not only reflects China’s strategic thinking in responding to internal and external challenges, but also provides an important path for promoting the modernization of national governance. Through continuous exploration and practice, deepening governance innovation will lay the foundation for achieving higher levels of national identity and social harmony.