The mesoscopic structure of real soil consists of numerous particles with different sizes, and yet the traditional reconstruction method of quartet structure generation set (QSGS) produces relatively uniform soil particles，which has significant discrepancy with the actual mesoscopic structure of soil. In order to remedy this deficiency, the QSGS is improved by considering the influences of porosity and autocorrelative function of soil, so that the mesoscopic structure reconfiguration closer to real soil is obtained. Based on the reconfiguration model combined with Lattice Boltzmann method , the D2Q9 model is applied to construct a two dimensional model for simulating mesoscopic seepage field of reconfiguration soil by setting the non-equilibrium extrapolation scheme at the inlet and outlet boundaries, and the bounce-back scheme at the soil particles’ boundary as well as the left and right boundaries. Meanwhile, according to a case study, a corresponding program is developed to simulate mesoscopic seepage field of reconstructed soil with constant inlet seepage velocity. The results show that the pore fluid preferentially flows through the channel with good connectivity. Meanwhile, the flow velocity is controlled by the whole connectivity of the channel. The velocity is much faster in whole-through-channel than that in partial-through-channel. Even if there exists a large pore space, the velocity still depends on whether or not it is on the channel with integral connectivity.