This study proposes a comprehensive topology optimization framework for district energy systems, integrating numerical modeling with advanced optimization techniques to improve system reliability and cost-efficiency. The framework focuses on key optimization variables. The primary objective is to minimize both capital and operational expenditures by leveraging nonlinear numerical simulations. A topology optimization approach is employed to solve the resulting nonlinear problem efficiently. To address the challenge of thermal demand satisfaction for a large number of buildings, a constraint expression is implemented, which reduces computational complexity while ensuring accurate load delivery to 146 buildings across the system. The optimization framework is developed and executed using a numerical modeling tool, allowing for precise simulation of hydraulic and thermal behaviors in the district energy system. Simulation results demonstrate significant improvements in both economic and performance metrics: pipe costs are reduced by approximately 17.14%, pumping costs are lowered by 91%, and overall system efficiency increases from 89% to 92%. These outcomes highlight the potential of the proposed methodology to deliver a scalable and practical solution for district energy system planning and retrofitting. Moreover, the integration of planning, numerical simulation, and enhancement workflows contributes to the development of digital twin technologies for urban thermal infrastructure, enabling data-driven decision-making and future scalability. The framework provides a robust foundation for optimizing district energy systems in both existing and newly planned urban environments.