The development of disruptive technological innovation has become a significant strategic direction in our country. To adapt to this need, special arrangements are required in various aspects, such as institutions and personnel, along with the establishment of project management mechanisms that align with the demands of disruptive technological innovation. This paper is based on the incentive and supervision model of principal-agent theory, constructing a four-stage analytical framework for scientific and technological project management. By conducting a comprehensive analysis of the selection, incentives, supervision, and support processes for project managers at the Defense Advanced Research Projects Agency (DARPA), recommendations are proposed for project management in the process of developing disruptive technological innovation in our country. The aim is to accelerate the enhancement of effectiveness in disruptive technological innovation, promote reforms in the scientific and technological system, and provide theoretical and practical experience support.