Interdisciplinary projects are a powerful tool for advancing scientific and technological innovation in any country. However, in China, such projects heavily rely on government and university funding, creating a challenging dependency. Once funding is withdrawn, it becomes difficult for many interdisciplinary projects to sustain themselves. To address this issue, this study uses the "Unfreeze—Transformation—Refreeze" framework to analyze transformation pathways of interdisciplinary projects. The research focuses on nine successful and three failed interdisciplinary projects under the U.S. National Science Foundation's Engineering Research Centers. Through multiple case studies and fuzzy−set qualitative comparative analysis, this study identifies key transformation paths. The findings reveal that successful transformation of interdisciplinary projects requires focused attention during the unfreezing phase, progressive reforms and diversified funding acquisition during the transformation phase, and institutional development during the refreezing phase. This study outlines a four−pronged pathway to strengthen China's multidisciplinary research−funding architecture. First, establish a durable, predictable funding framework that provides long−term support and reduces policy volatility. Second, enable local governments to deploy context−sensitive instruments aligned with regional strengths and needs. Third, refine universities’ internal governance to curb fragmentation and reward collaboration. Finally, and most critically, build a three−tier industry–academia–research consortium to achieve coordinated action, integrate resource and reach a consensus.