The performance of the innovative configurations of the “efficient” thermal networks is a key topic in scientific research, focusing on distribution temperatures and integration with high-efficiency plants and renewable sources. As it already happens for the electricity prosumers, a thermal prosumer may feed the district heating network through a bidirectional exchange substation with the excess of the locally produced thermal energy (e.g., by means of solar thermal plant) or with the waste heat recovered in the industrial processes. The Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) and the Alma Mater Studiorum University of Bologna (UNIBO) designed a bidirectional substation prototype, based on a return-to-supply configuration, and tested steady-state and dynamic conditions to evaluate performances and optimization measures. In this paper, the Modelica language and Dymola software were used to run a multi-domain simulation and model-based design of the substation, starting from a new heat exchanger model featuring variable efficiency, based on the thermal resistance scaling method. Control systems and components were customized from models in standard libraries in order to reproduce the substation behavior under defined operating settings, and the model was validated on the abovementioned experimental tests. Numerical results in terms of exchanged powers, temperatures and flow rates were systematically compared to experimental data, demonstrating a sufficient agreement. In particular, the absolute mean deviation—in terms of temperature—between experimental and numerical data assessed over the entire tests remains contained in +/−1 °C. As further step of the analysis, an optimized model could be included as a component in a district heating network for further investigations on the prosumers’ effects on an existing traditional grid (e.g., in case of deep renovation of urban areas connected to district heating and/or creation of micro energy communities).