In the present study, modeling of two-phase flow through porous medium is performed by Lattice Boltzmann method; moreover, the porous medium with different porosity ratio are examined. The Shan–Chen-type (SC) multiphase lattice Boltzmann model at D2Q9 network is used to simulate the two phase flow. To validate the used Fortran code in the simulations, first, two-phase flow in channel with hydrophobic and hydrophilic surface, and then a droplet on the surface with different hydrophilic and hydrophobic are simulated. Achieving optimized array of porous medium which reduces the leakage flow rate and fluid penetration was the primary aim of our study. To achieve the mentioned purpose, first, the flow penetration through different porous medium arrays is compared; then, effect of hydrophobicity on penetration is studied. Finally, the leakage flow rate of various arrays is investigated. The results indicate that utilizing a combined porous medium can drastically reduce the penetration and leakage. This optimized configuration has lower porosity in underneath part. Also, result show when the surface is hydrophobic, the penetration of fluid through the porous medium is slower, compared with the hydrophilic surface.