Mueller matrix imaging polarimeter (MMIP) can be used to measure the polarization aberration (PA) of a lithographic projector in the form of the Mueller pupil, while the Jones pupil is required for lithographic imaging simulations, projection lens design and PA evaluation. In this paper, a Jones pupil measurement method of lithographic projection lens is proposed. The measurement device of the method is the same as an MMIP, but a new polarimetric measurement equation is derived to solve the Jones pupil directly from the Kronecker product of the Jones matrix and the measured intensities. Two new polarimeter configurations with the minimum condition number are designed to further improve the accuracy in the presence of error sources. The performance of the method is evaluated by measurement errors of a typical Jones pupil in the presence of error sources. Comparisons between the proposed method and the conventional method, in which the Jones pupil is converted from the Mueller pupil measured by MMIP, are given. The results validate that the measurement accuracy of the Jones pupil is significantly improved without increasing the complexity of existing measurement systems.