The quartet structure generation set （QSGS）， as well as improved QSGS， were used to equivalently reconstruct the three-dimension（3D） isotropy and anisotropy pore structure of the real soil. Combined with the lattice Boltzmann method （LBM）， the numerical simulation of the seepage field employing the MATLAB automatic program was carried out to explore the influence of different pore parameters and model anisotropy on seepage characteristics. The results showed that when the mesh size of the 3D model was 100×100×100， the maximum increase of pore connectivity rate nc reached 19.23 %. The fluid preferred to form the main seepage channel in the position with good connectivity and large pore throat diameter， and there was a “finger-in” effect. The closer the fluid was to the axis of the channel， the greater the flow velocity was. The calculated permeability k of 3D reconstructed soil increased with the increase of model porosity n and decreased with the decrease of soil particle size. When the distribution probability Pc was 0~0.05， the permeability k decreased significantly， and the reduction was 42.86%. The seepage velocity at the outlet boundary of the reconstructed model considering anisotropy fluctuated greatly and irregularly. The streamline distribution streamline sparse and interlaced， with no prominent main seepage channel. This study can better reveal the flow law of fluid in the 3D pore structure and provide some references for the research methods of 3D soil reconstruction and meso-seepage simulation.