The paper deals with the problems arising in heterogeneous networks used in HPC systems based on the MPI. The main problems are the high complexity of configuring, adapting to dynamic changes and ensuring uniform data QoS characteristics for paths passing through subsystems implemented in accordance with various standards. A unified data transfer protocol and an approach to development such networks are proposed. This approach is based on the use of a unified router core. It can be used to form networks on a chip. Routers for local area networks can be combined by connecting various interface controllers to this core. Similarly, bridges between local networks, networks on a chip can be combined. The use of a unified protocol and a unified router core makes it possible to significantly simplify the network configuration process and ensure uniform QoS parameters. The feasibility, achievable characteristics of the proposed protocol and approach are evaluated.