This study presents a numerical method to coordinate membrane structure calculated by the phase-field method with direct numerical simulation of particulate flow. The immersed boundary method was used for coordination of the fluid computation; and level set method was used for coordination of the particle computation, which requires the distance between the membrane surface and the particles and the direction of fluid flow. The coordinated simulation was then applied to the permeation of a single particle through two types of membrane structures. First, the phase field method was used to prepare two types of membranes with differing phase separation times, then direct numerical simulation was performed for the permeation of a single particle through these membranes. Markedly different particle velocities and permeation times were found between two types of membrane structures.