The cover-cut method within limited sites faces numerous technical and managerial challenges, so it is of great practical significance to study effective countermeasures. This article takes a new metro project as an example, and integrates refined organizational management with key technological optimizations to assess the impact of site conditions on the allocation of construction resources. A construction management organizational approach based on spatiotemporal effect analysis is established. By detailing and subdividing the construction process and work units, merging similar management stages, and optimizing critical processes through technical means, the construction period is shortened, and efficiency is increased. The effectiveness of the proposed approach is validated through an actual engineering case: after implementing the optimization measures, the early construction period of the cover-cut method was saved by 4.9 days, the mechanical utilization rate was increased by 16.7% , and the comprehensive cost was reduced by 11.1%. The results show that this study ensures project quality and public safety in practice, enhances construction efficiency, and provides a reference for the early stage of the cover-cut method under similarly limited sites conditions.