The paper presents the results of the development of a model of a heat exchange system with a bypass connection of flows. An analytical model of a bypass for two heat exchange elements in the form of a relationship between the temperature ratio differences of flows and efficiency has been developed. The resulting expression for the efficiency of energy exchange in the system depends on the distribution of elements and flows at the entrance to the system and does not depend on the distribution in the mixing unit. It is shown that the key factor determining both the operation of the designed system and its elements is the correspondence of the direction of the processes in the real system with their direction, hypothetically chosen by the designer when specifying its topology. The distribution of the energy potential dictates the conditions for the operability of the system and its elements through the uncertainty of the values of the average energy measures. The statement of the problem of determining the matrix elements that satisfy the requirement of the minimum uncertainty of the average energy measures leads to the determination of the distribution of the efficiency of the system elements in its topological representation in accordance with the requirements of the second law of thermodynamics. The formulated requirements for the minimality of the uncertainty of the average energy measures and the construction, based on the Shannon principle, make it possible to obtain a solution to the formulated problem as a finite subset of the values of the efficiency of the inter-network and intra-network energy exchange. In addition, the extremeness of solutions (minimum uncertainty of average energy measures) ensures the maximum efficiency of energy transfer from the “hot” network to the “cold” network in its elements and the minimum energy dissipation in the mixing nodes. The urgency of the topic is due to the fundamental need to reduce energy costs of systems. The applied aspect is to minimize the mass, dimensions and energy component in enterprises where thermal transformations are significant.