The control and management of water leakage at subway stations have long been key research issues in the subway field, determining the service life and functionality of subway systems. Based on the characterization methods of subway station waterproofing systems and the leakage mechanism, leakage control measures were proposed that are suitable for both the construction and operational phases. Furong East Road Station on Metro Line 8 in Xi' an was selected as a case study, and numerical simulations were conducted using finite element software Midas Fea NX and Midas GTX to verify the effectiveness of leakage prevention and control during the construction and operational phases. The research findings show that, during construction, adjusting the pouring interval can reduce thermal stress generated by cement hydration. When the interval exceeds 120 hours, the risk of concrete cracking is relatively low, with a crack rate remaining below 3%. A leakage treatment measure is proposed for the operational phase, which involves the installation of pre-embedded grouting pipes and a specific layout method. This facilitates quick grouting and leakage sealing when leakage occurs during operation. This method enables fast and efficient treatment during the early stages of leakage and is validated through both practical engineering and numerical modeling. The result provides important references for ensuring the structural safety and service life of subway systems.