Abstract: Applied basic research is an important category of research in the "Pasteur Quadrant" and a crucial type of research for solving key technological principles and scientific problems. Joint Funds represent a government-led, organized, and demand-oriented critical mechanism for funding applied basic research. Based on principal-agent theory, this study examines the multi-level principal-agent relationships among the National Natural Science Foundation of China (NSFC), joint funders, scientific experts, research institutions, and researchers during Joint Fund implementation through the analytical framework of "process-content-institution-environment". The study found that the main reasons affecting the effectiveness of joint fund funding are: differences in the translation of technical and scientific problems, information asymmetry leading to insufficient selection of research partners and supervision of scientific research results, blurred boundaries of cross-border organizations, and the need to improve governance capabilities. Considering the particularity of applied basic research, the joint fund should optimize the agency model, strengthen the construction and governance capabilities of boundary organizations, enhance the participation and scope of joint funders, establish and improve evaluation mechanisms and differentiated management systems, and enhance the independent innovation capabilities of joint funders.