Significant post-construction settlement will be induced under the action of cyclic traffic load in saturated soft soil subgrade and it is also responsible for most differential settlement. To predict the long-term settlement of subgrade, experiential explicit constitutive models based on cyclic triaxial test or hollow cylinder test is combined with equivalent finite element method and it has achieved good effect. The pore pressure model used above is accumulating instantly and dissipating gradually, but the true pore pressure model is accumulation and dissipation proceeding simultaneously. This difference between them will make the settlement calculated by older pore water pressure model be smaller than normal. This paper improves the pore pressure model used currently by applying an analytical expression which can reflect the rules of pore pressure accumulation and dissipation under condition of vibration and natural drainage; and the improved model is used to predict the long-term settlement of the first runway subgrade in Shanghai Pudong International Airport. Compared with the current model’s result, the result based on improved model is closer to the measured actual data.