The challenges arising from the management of municipal solid waste (MSW) have a profound impact on the sustainable development of urban areas. As a sustainable solution, the transportation of MSW underground offers the potential to alleviate traffic congestion and reduce environmental pollution. In this study, we propose the implementation of a large-scale underground waste collection system (UWCS). To begin, a comprehensive operational process for the UWCS is designed based on an intelligent technology system, including facility operation, processing workflow, and technical parameters. Additionally, network planning methods for the UWCS are presented. A mixed-integer linear programming model is formulated with the objective of minimizing total cost. This model determines the optimal location and allocation of nodes within the network, as well as the pipeline layout and flow direction. Given the computational complexity, a hybrid optimization method, namely the genetic greedy algorithms and genetic variable neighborhood search algorithms (GGA-GVNS), is devised to obtain high-quality solutions for the model. Finally, to validate the efficacy of the proposed method, a simulation is conducted in the central city of Nanjing, China. The results demonstrate that the implementation of the UWCS network in Nanjing’s city center can yield an annual benefit of USD 5.99 million. Moreover, a sensitivity analysis reveals further MSW management-related insights and long-term planning strategies.