Government funding plays an important role in building a multi-channel pattern of sustained and stable investment in basic research. As a special type of China’s national natural science fund, the joint fund has made long-term and in-depth exploration and practice in the aspects of meeting the national demand, guiding diversified input, promoting resource sharing and multilateral cooperation, and has achieved good results. However, the existing literature is weak on the internal mechanism of multi-investment guided by joint funds. From the “joint funding project” to the “joint fund”, the development of the joint funding can be divided into four stages, with different features of function positioning, funding methods and institutional arrangements in each stage. The inherent logic of the joint fund guiding diversified investment includes two aspects. First, the joint fund has realized the expansion of the functions of the National Natural Science Foundation (NSFC) in terms of funding sources, scientific research infrastructure and social services. Second, from the basic premise of cooperation, internal motivation and platform guarantee, the joint fund promotes the complementary advantages of the NSFC and diversified investment subjects. The fundamental reason for the success of the joint fund is to realize the efficient and accurate docking of “application target-scientific problem-capital investment-scientific research force”. Finally, the joint fund is faced with the challenges of coordinating unified management and unique needs, shaping the management system adapted to its characteristics, and breaking through the “public-private” boundary of the investment subject, which still needs further reform and innovation.