The increasing energy crisis and environmental problems promote the development of distributed energy systems (DESs) that utilize combined heat and power technology, renewable energy technology, and waste heat recovery technology to meet various load requirements. Although there is existing work and research on a variety of DESs, most previous studies tend to focus on energy production with little consideration of a distributed energy network and its energy loss, which results in large errors in energy-efficiency calculations and performance analyses. In this paper, a new DES model is proposed with full consideration of an energy network and the full use of solar energy, terrestrial heat, and exhaust gases. At the same time, an effective bi-level optimization method is also proposed for the daily operation of the DES in order to improve the system performance and benefits in the energy, the economy, and the environment. Specifically, the co-generation energy station and water heating network in the DES are optimized separately with two different optimization models. The first-level optimization model is used to seek the optimal values of water mass flow rate and water temperature of the water heating network, and the second-level optimization model is built to determine the optimal energy purchasing strategy and the optimal energy outputs of the co-generation energy station. In order to verify the advantages and effectiveness of the proposed system and method, a contrastive simulation study is undertaken to provide a comparison of the global optimization method. Simulation results show that energy loss, energy cost, and energy consumption of the DES using the bi-level optimization operation strategy only account for 22.51%, 33.42%, and 51.31% of the quantities of the global optimization method, respectively. The hourly curves of the optimal operating variables also demonstrate that the proposed bi-level optimization method can improve the operating stability of the DES better than the global optimization method.