Seepage of shield tunnel occurs occasionally in the weak and water-rich stratum after long-term use, which has impact on the dissipation of excess pore water pressure caused by shield construction. Thus, tunnel seepage conditions cannot be ignored in the calculation of long-term surface settlement. On the basis of the previous research, a calculation method that can evaluate long-term consolidation settlement in the weak and water-rich stratum was proposed, considering that the dissipation of excess pore pressure is caused by the seepage of groundwater towards the lower head position in stratum and the position of shield tunnel. For three actual projects, the proposed calculation method is compared with the method that does not consider the tunnel seepage as well as the actual measurement results. The results show that computed result by the method without considering tunnel leakage is smaller than the measured value in the stratum with high clay content. Additionally, the larger the seepage volume, the greater the surface settlement; Considering tunnel seepage can effectively improve the calculation accuracy of long-term settlement, which verifies the reliability of the proposed calculation method.