Abstract: Objective To analyze and summarize the experience and practices of the special fund management of the National Key Research and Development Program(NKRDP)and put forward targeted methods and suggestions. Method A series of issues related to the budgeting, budget execution and funding adjustments involved in the implementation of NKRDP that National Center for Women and Children's Health of China CDC has been undertaking for recent 5 years, and specific methods and suggestions were put forward. Result In the process of funding management of NKRDP, it needs the joint participation of the research group and financial personnel, detailed budget preparation, strict implementation of the budget, open and transparent process management. It is also important to establish an effective communication mechanism between the internal scientific research funding management policies and departments. Conclusion NKRDP have a large amount of funds and high funding management requirements. It requires the participation of multiple personnel and strict management and budget implementation. Only by this way can the usage efficiency of the special funds of NKRDP be improved, so as to ensure the realization of the overall objectives project of the program.