Over the past few decades, the scientific and technological cooperation and economic and trade cooperation between China and the US have together shaped the “China-US innovation system”. The “China-US innovation system” is undergoing a shift from “complementary” to “competitive”, even in some fields, there is a tendency towards a “struggle-oriented” approach. This transformation is driven by both technological revolution, digital transformation, and geopolitical instability leading to “separation”, as well as stable factors of “win-win” cooperation generated by the laws of technological development, global economic structure, market mechanisms, and global challenges. From the perspective of the economic cycle triggered by the technological revolution, the institutional conflicts, adjustments and adaptations of the “China-US innovation system” around scientific and technological competition and cooperation will continue. The stability and development of the China-US innovation system will benefit both countries and contribute to global economic recovery and innovation. Therefore, the two countries should take a long-term view, adhere to the principles of openness, cooperation and inclusiveness, and jointly promote the sound development of the system in terms of promoting interaction between innovation subjects and opening up innovation resources.