We analyze a heterogeneity of the educational system on the basis of one parameter: input grades of university students. We propose a mathematical model based on the construction of universities’ interval order. We use the Hamming distance to evaluate the heterogeneity of the educational system, and the Unified State Examination (USE) scores of Russian students to illustrate the application of the model. We show that institutions taking weak students turn the whole system of universities into a poorly structured nonhomogeneous system. In contrast, after deleting the weakest part, the remaining set of universities becomes a well-structured system.