An in-situ measurement method of polarization aberration (PA) in lithographic projection lens is proposed. A new characterization of PA is proposed, and a cross-correlation relationship among three Pauli terms of PA and the difference in aerial images under three pairs of orthogonal illuminated polarization states is derived. Based on this, the principal component analysis is performed on three groups of differential aerial images of alt-phase-shift mask to solve all the Pauli Zernike coefficients of PA. This paper describes the coupling of different Pauli terms theoretically in the imaging process and resolves the coupling problem through the principle of measurement based on this theory. As a result, first 37 orders of Zernike coefficients for all Pauli terms can be measured by the proposed method. In the condition of typical deep ultraviolet lithography, random PA tests of the proposed method are performed and the standard errors of 6×37 measured Pauli-Zernike coefficients (real and imaginary parts of three Pauli terms) are all in the order of 10 -3. Simulation results validate the correctness and the effectiveness of the proposed method.