To answer the problem of ambiguous design levels for large-scale distributed simulation systems, this paper proposes a hierarchical system model based on the quotient space theory. This model consists of a system global design level, an architecture level, and a execution structure level to solve the problem of diverse levels on system design. Furthermore, we deeply analyze the relationship between the granules of different levels in both horizontal and vertical directions, and integratedly consider simulation tasks, resources and services. Finally, the model is verified based on a real simulation system design example, and the results illustrate that the flexibility and reusability of the system can be improved with the application of the hierarchical design model.