On the basis of the generalized diffraction integral formula for misaligned optical systems in the spatial domain, an analytical propagation expression for the elements of the cross-spectral density matrix of a random electromagnetic beam passing through a misaligned optical system in turbulent atmosphere is derived. Some analyses are illustrated by numerical examples relating to changes in the state of polarization of an electromagnetic Gaussian Schell-model beam propagating through such an optical system. It is shown that the misalignment has a significant influence on the intensity profile and the state of polarization of the beam, but the influence becomes smaller for the beam propagating in strong turbulent atmosphere. The method in this paper can be applied for sources that are either isotropic or anisotropic. It is shown that the isotropic sources and the anisotropic sources have different polarization properties on beam propagation.