Abstract Polarization and spatial coherence of quantization Gaussian Schell-beams propagating through the anisotropic non-Kolmogorov turbulence of marine-atmosphere channel are studied based on the quantized Huygens–Fresnel principle and the degree of quantum polarization. The spatial coherence length and the polarization degree of linearly polarization quantization Gaussian Schell-beams are developed. The effects of outer scale on the lateral coherence length are not obvious as same as the effects of wavelength on the degree of polarization. The degree of polarization decreases as the source transverse coherent width, anisotropic factor, the number of received photons, spectral index, the inner scale of turbulent eddies and source transverse radius decrease or generalized refractive-index structure parameter increases. The refractive-index structure parameter, spectral index and inner scale have also effect on the changes of lateral coherence length. Those results can be used to improve the performance of a polarization-encoded quantum communication system.