Polarization properties of electromagnetic Gaussian Schell-model beams propagating through the anisotropic non-Kolmogorov turbulence of marine-atmosphere channel are studied based on the cross-spectral density matrix. Detailed analysis shows that the average polarization decreases with increasing the spectral index, inner scale of turbulence and generalized refractive-index structure parameter. We find the effects of anisotropic turbulence on the average polarization is less than that of the isotropic turbulence and the depolarization effect of turbulence in marine-atmosphere is larger than terrene-atmosphere. The electromagnetic Gaussian Schell-model beam with the parameters of smaller σxx ,σyy and Ax, but larger Ay will reduce the interference of turbulence.