Abstract: After three decades of practice and exploring, the National Natural Science Foundation of China has accumulated successful experiences for the management of the interest-oriented research funding. However, it still needs to further explore the management of organized innovation facing to the nation’s major needs. To lead the scientists to combine the interest-oriented research and the one facing to the nation’s major needs, solving the problem of “stuck neck” in the science and technology, the department of Management Sciences had implemented reforms through launching and management of a series of special projects in recent years. It had explored the mechanism for proposing the scientific questions for the national major needs, i.e. “Six steps”, and the mode for the organized innovation, so that to produce research achievements that could be effectively employed in practice. These serve for the aim of basic research effectively promoting the high-quality development of China.