Firstly, we discussed concepts of system, continuous system, discrete system, project, scientific research project, and university scientific research project system. Then we studied the discreteness of the project system, concluded basic features of scientific research projects, put forward the concept of project system discreteness, and analyzed the contradiction between the ideal and practical conditions of the project system. We also presented the contradiction between the expected continuity and the practical dispersion of the project system from the perspective of epistemology, which was the result of objective law. This contradiction can be unified with the technological innovation. Finally, we put forward key points of the scientific research management with the project system dispersion.