The traffic load transfers from track, roadbed, and tunnel structure to foundation, generating cyclic dynamic stress and excess pore water pressure in soil, inducing settlement of shield tunnel. A vertical coupling dynamical model of metro train, track, tunnel and foundation is developed and used to analyze the effect of differential settlement of tunnel foundation on subway traffic load. A three-dimensional numerical model is established based on the engineering background of the subway tunnel near the Stadium Station of Shanghai Metro Line 1. Combined with the calculation formulas of accumulated plastic strain and cumulative pore pressure, the influence of train speed on the long-term settlement of subway foundation without tunnel uneven deformation is analyzed and compared to the case with tunnel differential deformation. It is shown that the larger the amplitude of soil vibration is, the faster the amplitude attenuation becomes while the train speed gradually increases. The longitudinal differential settlement has significant adverse effect on the operation of subway tunnel. As the train speed increases, this effect becomes more significant. When the tunnel differential settlement is small and the track condition is good, tunnel operation settlement decreases as the metro driving speed increases. However, the long-term settlement of tunnel significantly increases as vehicle speed increases, while the foundation differential settlement becomes pronounced and the track irregularities are significant.