Reveal the characteristic of surface settlement and soil deformation during the pipe-jacking under real strata, a modeling method of real and complex strata was proposed in this study. Based on a diversion project in a city, this paper conducted the three-dimensional numerical simulation of pipe-jacking construction in real complex strata and simplified strata. The simulated results of surface settlement in the real and complex strata agree very well with the field measurement results, while the settlement obtained from the simulation in simplified and uniform strata disagreed with the settlement from in-situ measurement. The simulated displacement of soil above the pipe goes down and the displacement below the pipe goes down, of which the value was related to the mechanical behavior and geometric distribution of strata. The lateral displacement of soil above the pipe is basically oriented toward the pipe jacking axis, and the spatial distribution of soil has no effect on the value. However, the spatial distribution of soil significantly effects the lateral deformation of soil below the pipe jacking. The complex strata significantly influence the value of surface settlement. However, the lateral range of surface settlement is ±5.3D (D the pipe diameter), and is significantly influenced by the distribution of complex strata.