This paper develops and validates a methodology for rigorously modeling the pattern transfer in alternating Phase Shift Mask (altPSM) process by incorporating mask structure, partially coherent illumination, polarization and resist in a full-vector electromagnetic (EM) model. Mask topography is included in EM simulation to solve for the field immediately after the mask. To model the partially coherent illumination, the light source is decomposed into a set of plane waves with different angles of incidence on mask. Each wave requires an EMF simulation over the mask. A perturbation approach is developed in this paper to reduce the EM simulation time by over 50%, thus enabling the vector model of partial coherence. Then the field after mask is decomposed into TE and TM polarized waves so as to calculate the field in resist/BARC/silicon multilayer. At high NA, this full vector model is needed to investigate altPSM because there exists appreciable difference between the images due to TE and TM waves. TM wave degrades more severely in resist, thus TE is more desirable. The experiments were conducted at Tokyo Electron Texas LLC. on a 248nm KrF stepper, NA 0.6, σ 0.3. Both experiments and simulations show that transmission imbalance depends on defocus. When the focal plane is moved towards the lens, the 180° space can be brighter than 0°.The 0° space is more sensitive to defocus and has larger CD variation than 180° does. Finally the simulated patterns are compared with experimental SEM picture.