Abstract:In recent years, some serious problems have occurred from time to time in the supervision of funds for science and technology projects, such as the non-earmarking of special funds, fraud, interception, misuse and misappropriation of special funds, etc. In order to further prevent and resolve the risk of fund use, curb the signs of danger, promote the diversification of supervision methods, take full advantage of information technology and commercial bank service resources, and realize the whole process of fund use trace management, this paper draws on relevant domestic and foreign experiences, aimed to explore an innovative mechanism to improve fund management of science and technology projects from the source, and proposed to establish a management mode of special fund sub-account of national science and technology plan in China, so as to effectively safeguard the security of national financial funds with less management costs and optimize the innovation environment.