In order to study the stratum disturbance law caused by shield tunneling under complicated stratum conditions， a simulation method of shield tunneling considering the three-dimensional spatial distribution of the stratum is proposed. This method uses the Kriging algorithm to construct a 3D geological model. The 3D geological information is then integrated into a finite element model via a conditional judgment algorithm， so as to facilitate the numerical simulation of shield tunneling with 3D geological information. According to the proposed method， a pre-processing program for the simulation of shield tunneling in complex strata is developed by C# language. A case study of the Changsha Metro Line 4 project is illustrated here. Three sections with different stratum conditions were chosen. And the excavation process of the earth pressure balance shield （EPBS） machine was simulated by pre-processing program with different proportions of extremely soft rock， soft rock， and hard rock in the shield tunneling face. Simulation results reveal that the increase in the proportion of extremely soft rock in the shield tunneling face can lead to a significant increase in the final surface settlement. Compared with the tunnel section with a 50% proportion of extremely soft rock， the final ground settlement at the full-sectional extremely soft rock was increased by 11.67 mm. This finding is consistent with the measured data， verifying the effectiveness of the proposed method.