The accurate prediction of the permeability is the key to optimizing the molding process of fiber reinforced composites, thus to improve the composite quality, and reduce the material and labor costs in the manufacturing process. In this paper, the permeability of 2.5D woven preform with shear deformation was studied by experiments and numerical simulations. The permeabilities of the samples under various shear angles were measured by the radial flow method. An RVE (representative volume element) model based on the fabric microstructure and shear deformation is developed to predict the permeability of preform and the simulation results are compared with experiments value to verify the effectiveness of this model. Using this model, the effect of the fiber volume fraction on the permeability of the 2.5D woven preform was determined. Based on the structural characteristics, experimental and simulation results of the 2.5D woven preform, an empirical equation for predicting its permeability under shear deformation was formulated. The prediction accuracy of the equation was evaluated, and the equation was used to determine the change of permeability with shear deformation for the 2.5D woven preform.