Shield construction in structural soft soils inevitably disturbs the soil around the tunnel leading to tunnel settlement instead of tunnel uplift due to soil unloading rebound during construction. In this paper, tunnel settlement prediction in structural soft soils during construction has been studied by adopting Oujiang Beikou shield tunnel as an example. Firstly, disturbance degree calculation method based on effective stress was introduced and the disturbance degree due to shield construction was numerically simulated. Secondly, combined with one-dimensional consolidation test results, a “two-fold line” settlement calculation model was developed for disturbed soil. Finally, tunnel settlement during construction was predicted through one-way compression layer-summation method and compared with experimentally measured results. Research results demonstrated that the developed method was suitable for the prediction of shield tunnel settlement in structural soft soils.