Abstract: The deep drainage pipelines experience significant settlement during operation due to the long-term cyclic loading from water filling and discharge, potentially leading to pipe leakage and damage, consequently affecting the normal operation of the deep tunnel drainage system and environmental safety. To address the settlement issue of pipelines in soft soils caused by the long-term cyclic loading from water filling and discharge, a quasi-static finite element method is employed to simulate the stress distribution in the foundation induced by full-flow loads on the pipeline. Based on the layered summation method and empirical formulas for plastic strain and pore pressure accumulation with loading cycles in soft soils, a method for calculating the long-term settlement of the soft soil foundation beneath the pipeline is proposed. This method is used to predict the long-term settlement of the deep pipelines in the Suzhou River section of Shanghai, and the evolution laws of settlement in the pipeline-foundation system under untreated conditions of the bottom foundation are analyzed. The results indicate that due to the low-frequency heavy loading characteristics of water filling and discharge cycles, the settlement induced by the cumulative plastic strain in the foundation soils accounts for the vast majority. In contrast, the consolidation settlement caused by pore pressure dissipation can be almost ignored. The research findings can provide references for the design and operation safety assurance of deep tunnel drainage systems in soft soil areas.