With the rapid growth of China’s scientific and technological (S&T) investments and outputs, optimizing funding strategies to advance S&T breakthroughs has become a key challenge. This study analyzes 552 survey responses from recipients of the National Natural Science Award and the Technological Invention Award (2008-2020) and employs qualitative comparative analysis (QCA) to investigate the collaborative mechanisms of curiosity-driven projects, mission-oriented projects, and enterprise-funded projects in driving breakthroughs. Drawing on five typical cases, the study develops a dynamic multi-funding coupling model, identifies two pathways through which national strategies and market demands can resonate, and highlights the flexibility advantages of curiosity-driven projects. The findings suggest enhancing the supporting for basic research, initiating diverse investments, and enhancing the roles of universities in industry-academia collaborations and research institutes in addressing national strategic tasks.