Abstract: The water-filled acoustic transparent structure is one of the important structural types of underwater vehicles. When active sonar acts on the target vehicle, sound wave can penetrate the outer surface of this structure and enter the target’s interior to cause internal scattering which influences target strength. A modified planar element method suitable for prediction of target strength of acoustic transparent structures is proposed. This method assumes that the scattering field is approximately the superposition of the scattering fields of planar elements on the inner surface and the corresponding planar elements on the outer surface. The shielding pairs between the inner and outer plannar elements are determined by the Z-Buffer algorithm, while the transmission and reflection coefficients of the plannar elements are also considered. The two parts of scattering field are calculated separately by using the non-rigid planar element method, and then the total target strength is predicted after coherent superposition. This method considers the primary scattering of the inner surface of the water-filled acoustic transparent structure, so the physical concept is clear, and the prediction accuracy of plannar element method is improved. The correctness of the method is verified by a double-layer plate model. This method has been applied to the sail part of BeTSSi Ⅱ, which is a typical acoustic transparent structure. The prediction accuracy of the proposed method is verified by the target strength experiment of the sail shrinkage model.