An extension of the explicit moving particle semi-implicit (MPS) method is proposed for simulating free surface flow through a porous structure object. The model formulation is based on the local volume averaging equations, and the porous drag is given by a general closure function. It can compute the macroscopic behaviors of incompressible flows in porous media. Specifically, the present study addresses numerical difficulties of existing MPS models in two respects, namely the conservation of macroscopic fluid volume and the well-balanced hydrostatic equilibrium where the fluid and porous media interpenetrate. Numerical tests are performed to examine the validity and accuracy of the proposed model, from which good agreements are found between the simulation results and validation data. In comparison with existing models, it is also demonstrated that the numerical techniques developed in this study are important to obtain consistent predictions of flow behaviors. Therefore, the present MPS method is shown to be suitable for modeling free surface flows interacting with porous structures.