With the continuous shrink of feature sizes, the 3D mask effects cannot be ignored in computational lithography. 3D mask effects inducing focus shift and scalar aberration like spherical aberration have been studied very well. To our knowledge, the polarization aberration (PA) including scalar aberration, retardance and diattenuation caused by 3D mask effects have not been paid attention to, which is very significant for computational lithography in advanced node. In this paper, we propose a novel approach to derive the PA induced by 3D mask effects from the diffraction frequency spectrum between the rigorous electromagnetic field model and the Kirchhoff model and express it as Jones matrix pupil. In addition, the physical decomposition of Jones matrix is adopted to obtain five physical properties of polarization aberration induced by 3D mask. Thus, the proposed method can fully, quantitatively, and clearly describe the PA induced by 3D mask.