Abstract: The newly revised Mineral Resources Law of 2024 incorporates into its statutory scope the strengthening of mineral resource and ecological environment protection, the promotion of high-quality development of the mining industry, and the safeguarding of national mineral resource security. From the legislative level, it further specifies the institutional arrangements concerning the approval of overlying strategic mineral resources and the special protection of strategic mineral resources, thereby elevating the functional positioning of overlying approval to the strategic height of national resource security. Against this backdrop, in order to coordinate the relationship between strategic mineral resource protection and factor assurance for major construction projects, harmonize the spatial configuration of mineral resource exploration and development with the implementation of major engineering construction, and strengthen resource protection and rational utilization, this study reviews the management evolution of mineral resource overlying by construction projects through institutional review and case analysis, with a focus on the key aspects of “planning embedding for source prevention”, the approval objects, timeframes, procedures, and project categories of overlying approval, as well as the effective coordination of related work. The paper provides an in-depth analysis of the reform transitions in mineral resource overlying management and the current dilemmas in concurrent approval, conclusion of compensation agreements, differentiated management, tracking and supervision mechanisms, and value accounting. Furthermore, it explores the ecological constraints and flexible balance under the framework of the new Mineral Resources Law, examines the reform practice of “consolidated multi-approval”, summarizes local cases, and distills replicable and generalizable reform experiences. Finally, targeted recommendations are proposed from five dimensions—streamlining approval procedures, optimizing compensation management, applying the principle of differentiated treatment, refining accountability, and strengthening evaluation mechanisms—providing useful practical references for mineral resource overlying management in the new era.