Precise ascertainment of the diffusion coefficient as the index of penetration of one species through another is essential for accurate physical modeling. The most precise and careful method for computation of these properties is Molecular Dynamics (MD). Unfortunately these methods have huge computational cost. The aim of this article is to introduce a suitable mesoscopic method and an efficient algorithm for calculating diffusion coefficient using this method. In this study we use Dissipative Particle Dynamics (DPD) for calculating diffusion coefficient of the water and lipid through the biological bilayer membranes. Eventually we validate our results with MD simulation and also experimental results. Then we can conclude about this method that besides being efficient from point of computational cost, the proposed algorithm is an accurate method for calculating diffusion coefficient. Therefore using this method, we are able to study the equilibrium behavior of bilayer membranes like calculating diffusion coefficient which with Molecular Dynamics simulations, it maybe takes more than hundreds of times.