A three-dimensional model structure that allows considering interphase layer around permeable inclusions is developed to predict water vapor permeability in composite materials made of a matrix Poly(3-HydroxyButyrate-co-3-HydroxyValerate) (PHBV) including Wheat Straw Fiber (WSF) particles. About 500 two-phase structures corresponding to composites of different particles volume fractions (5.14−11.4−19.52 % v/v) generated using experimental particles’ size distribution have permitted to capture all the variability of the experimental material. These structures have served as a basis to create three-phase structures including interphase zone of altered polymer property surrounding each particle. Finite Element Method (FEM) applied on these structures has permitted to calculate the relative permeability (ratio between composite and neat matrix permeability P/Pm). The numerical results of the two-phase model are consistent with the experimental data for volume fraction lower than 11.4 %v/v but the large upturn of the experimental relative permeability for highest volume fraction is not well represented by the two-phase model. Among hypothesis made to explain model’s deviation, the presence of an interphase with its own transfer properties is numerically tested: numerical exploration made with the three-phase model proves that an interphase of 5 µm thick, with diffusivity of Di≥1×10−10 m2·s−1, would explain the large upturn of permeability at high volume fraction.