A Jones-pupil-based method for measuring the polarization aberrations of the lithographic projection lens is proposed. A measurement equation based on the Jones matrix is derived, and a linear relationship between the intensity vector and the Kronecker product of the Jones matrix is built. The polarization aberration in the form of Jones pupil can be directly measured by this linear relationship. Using a Jones pupil of the typical lithographic projection lens as a measurement object, the numerical simulation are conducted to validate the proposed method. In these simulations, the actual parameter errors between the polarization elements and the charge coupled device (CCD) are considered. Measurement errors of this method are also compared with the results converted from the conventional Mueller pupil metrology. For the same rotation-angle configuration of polarization elements, the measurement errors of the diattenuation and the retardance by the proposed method are reduced significantly compared with that by the conventional method. The simulation results show that the proposed method can greatly improve the measurement accuracy of the polarization aberrations in the form of Jones pupil, without increasing the complexity of the existing metrology system.