In order to study the propagation of polarized photons in free-space, the concept “virtual particles” is proposed with the model of multilayered atmosphere. Located at the dividing surface of two atmospheric layers, the “virtual particles” only change the step distance, but not affect the propagating direction or the polarization of photons. On this basis the Mie scattering model of polarized photons in the multilayered atmosphere is established. The Monte Carlo simulation of the propagation of polarized photons in the multilayered atmosphere is made based on the model. The results show that this model can explicitly reveal the changes and their rules of polarization of photons in all kinds of atmospheric propagating processes. Therefore it can provide support for free-space quantum communication and other related studies based on atmospheric propagation of polarized photons.