To address the constraints of limited urban sources and worsening surface traffic congestion, and to improve the operational efficiency and sustainability of urban logistics, the authors introduce a surface-underground integrated logistics system and develop a corresponding cost-benefit analysis framework for evaluating different underground logistics implementation modes. Three typical system configurations are identified: (1) mixed-use metro lines, (2) freight-passenger integrated metro systems, and (3) dedicated underground logistics corridors. Their operational mechanisms and applicable urban conditions are comparatively examined. Based on five benefit dimensions: (1) circulation economy, (2) emission reduction, (3) traffic mobility, (4) spatial utilization, and (5) emergency response capacity, a monetized evaluation model is considered to quantify system advantages. Further, from the perspectives of government decision-makers and logistics service providers, an economic evaluation method is proposed to support scheme selection. A case study of the Beijing Municipal Administrative Center demonstrates the feasibility of the proposed framework. The results indicate that: (1) the mixed-use metro mode features the lowest cost and is suitable for low-demand logistic contexts; (2) the freight-passenger integrated mode provides an effective balance between costs and benefit and is suitable for medium-demand conditions; and (3) the dedicated underground logistics corridors mode is most advantageous in high-demand scenarios, generating the highest external benefits and long-term economic returns. In particular, this mode yields a net present value of approximately 610 million CNY, showing strong investment potential and significant capacity to improve delivery efficiency and mitigate surface traffic congestion.